Yield improvement in plants

ABSTRACT

Polynucleotides and polypeptides incorporated into expression vectors are introduced into plants and were ectopically expressed. These polypeptides may confer at least one regulatory activity and increased yield, increased light use efficiency, increased photosynthetic capacity, increased photosynthetic rate, increased photosynthetic resource use efficiency, greater vigor, and/or greater biomass as compared to a control plant.

This application is a divisional of U.S. patent application Ser. No. 15/025,367, filed Mar. 28, 2016, which is the United States national stage entry under 35 U.S.C. § 371 of International Application No. PCT/US2014/060267, filed Oct. 13, 2014, which claims the benefit of U.S. Provisional Application No. 61/890,613, filed Oct. 14, 2013. The contents of these applications are each incorporated herein by reference in their entirety.

FIELD OF THE INVENTION

The present invention relates to plant genomics and plant improvement.

BACKGROUND OF THE INVENTION

A plant's phenotypic characteristics that enhance photosynthetic resource use efficiency may be controlled through a number of cellular processes. One important way to manipulate that control is by manipulating the characteristics or expression of regulatory proteins, proteins that influence the expression of a particular gene or sets of genes. For example, transformed or transgenic plants that comprise cells with altered levels of at least one selected regulatory polypeptide may possess advantageous or desirable traits, and strategies for manipulating traits by altering a plant cell's regulatory polypeptide content or expression level can result in plants and crops with commercially valuable properties. Examples of such trait manipulation include:

Increasing Canopy Photosynthesis to Increase Crop Yield.

Recent studies by crop physiologists have provided evidence that crop-canopy photosynthesis is correlated with crop yield, and that increasing canopy photosynthesis can increase crop yield (Long et al., 2006. Plant Cell Environ. 29:315-33; Murchie et al., 2009 New Phytol. 181:532-552; Zhu et al., 2010. Ann. Rev. Plant Biol. 61:235-261). Two overlapping strategies for increasing canopy photosynthesis have been proposed. The first recognizes great potential to increase canopy photosynthesis by improving multiple discrete reactions that currently limit photosynthetic capacity (reviewed in Zhu et al., 2010. supra). The second focuses upon improving plant physiological status during environmental conditions that limit the realization of photosynthetic capacity. It is important to distinguish this second goal from recent industry and academic screening for genes to improve stress tolerance. Arguably, these efforts may have identified genes that improve plant physiological status during severe stresses not typically experienced on productive acres (Jones, 2007. J. Exp. Bot. 58:119-130; Passioura, 2007. J. Exp. Bot. 58:113-117). In contrast, improving the efficiency with which photosynthesis operates relative to the availability of key resources of water, nitrogen and light, is thought to be more appropriate for improving yield on productive acres (Long et al., 1994. Ann. Rev. Plant Physiol. Plant Molec. Biol. 45:633-662; Morison et al., 2008. Philosophical Transactions of the Royal Society B: Biological Sciences 363:639-658; Passioura, 2007, supra).

Increasing Nitrogen Use Efficiency (NUE) to Increase Crop Yield.

There has been a large increase in food productivity over the past 50 years causing a decrease in world hunger despite a significant increase in population (Godfray et al., 2010. Science 327:812-818). A significant contribution to this increased yield was a 20-fold increase in the application of nitrogen fertilizers (Glass, 2003. Crit. Rev. Plant Sci. 22:453-470). About 85 million to 90 million metric tons of nitrogen are applied annually to soil, and this application rate is expected to increase to 240 million metric tons by 2050 (Good et al., 2004. Trends Plant Sci. 9:597-605). However, plants use only 30 to 40% of the applied nitrogen and the rest is lost through a combination of leaching, surface run-off, denitrification, volatilization, and microbial consumption (Frink et al., 1999. Proc. Natl. Acad. Sci. USA 96:1175-1180; Glass, 2003, supra; Good et al., 2004, supra; Raun and Johnson, 1999. Agron. J. 91:357-363). The loss of more than 60% of applied nitrogen can have serious environmental effects, such as groundwater contamination, anoxic coastal zones, and conversion to greenhouse gases. In addition, while most fertilizer components are mined (such as phosphates), inorganic nitrogen is derived from the energy intensive conversion of gaseous nitrogen to ammonia. Thus, the addition of nitrogen fertilizer is typically the highest single input cost for many crops, and since its production is energy intensive, the cost is dependent on the price of energy (Rothstein, 2007. Plant Cell 19:2695-2699). With an increasing demand for food from an increasing human population, agriculture yields must be increased at the same time as dependence on applied fertilizers is decreased. Therefore, to minimize nitrogen loss, reduce environmental pollution, and decrease input cost, it is crucial to develop crop varieties with higher nitrogen use efficiency (Garnett et al., 2009. Plant Cell Environ. 32:1272-1283; Hirel et al., 2007. J. Exp. Bot. 58:2369-2387; Lea and Azevedo, 2007. Ann. Appl. Biol. 151:269-275; Masclaux-Daubresse et al., 2010. Ann. Bot. 105:1141-1157; Moll et al., 1982. Agron. J. 74:562-564; Sylvester-Bradley and Kindred, 2009. J. Exp. Bot. 60:1939-1951).

Improving Water Use Efficiency (WUE) to Improve Yield.

Freshwater is a limited and dwindling global resource; therefore, improving the efficiency with which food and biofuel crops use water is a prerequisite for maintaining and improving yield (Karaba et al., 2007. Proc. Natl. Acad. Sci. USA. 104:15270-15275). WUE can be used to describe the relationship between water use and crop productivity over a range of time integrals. The basic physiological definition of WUE equates the ratio of photosynthesis (A) to transpiration (T) at a given moment in time, also referred to as transpiration efficiency. However, the WUE concept can be scaled significantly, for example, over the complete lifecycle of a crop, where biomass or yield can be expressed per cumulative total of water transpired from the canopy. Thus far, the engineering of major field crops for improved WUE with single genes has not yet been achieved (Karaba et al., 2007. supra). Regardless, increased yields of wheat cultivars bred for increased transpiration efficiency (the ratio of photosynthesis to transpiration) have provided important support for the proposition that crop yield can be increased over broad acres through improvement in crop water-use efficiency (Condon et al., 2004. J. Exp. Bot. 55:2447-2460).

Estimates of water-use efficiency integrated over the life of plant tissues can be derived from analysis of the ratio of the ¹³C carbon isotope to the ¹²C carbon isotope in those tissues. The theory that underlies this means to estimating WUE is that during photosynthesis, incorporation of ¹³C into the products of photosynthesis is slower than the lighter isotope ¹²C. Effectively, ¹³C is discriminated against relative to ¹²C during photosynthesis, an effect that is integrated over the life of the plant resulting in biomass with a distinct ¹³C/¹²C signature. Of the many steps in the photosynthetic process during which this discrimination occurs, discrimination at the active site of Rubisco is of most significance, a consequence of kinetic constraints associated with the ¹³CO₂ molecule being larger. Significantly, the discrimination by Rubisco is not constant, but varies depending on the CO₂ concentration within the leaf. At high CO₂ concentration discrimination by Rubisco is highest, however as CO₂ concentration decreases discrimination decreases. Because the CO₂ concentration within the leaf is overwhelmingly dependent on the balance between CO₂ influx through the stomatal pore and the rate of photosynthesis, and because the stomatal pore controls the rate of transpiration from the leaf, the ¹³C/¹²C isotopic signature of plant material provides an integrated record of the balance between transpiration and photosynthesis during the life of the plant and as such a surrogate measure of water-use efficiency (Farquhar et al. 1989. Annu. Rev. Plant Physiol. Plant Mol. Biol. 40:503-537).

With these needs in mind, new technologies for yield enhancement are required. In this disclosure, a phenotypic screening platform that directly measures photosynthetic capacity, water use efficiency, and nitrogen use efficiency of mature plants was used to discover advantageous properties conferred by ectopic expression of the described regulatory proteins in plants.

SUMMARY

The instant description is directed to a transgenic plant or plants that have increased photosynthetic resource use efficiency with respect to a control plant, or a plant part derived from such a plant, e.g., shoot vegetative organs/structures (e.g., leaves, stems and tubers), roots, flowers and floral organs/structures (e.g., bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (e.g., vascular tissue, ground tissue, and the like), pulped, pureed, ground-up, macerated or broken-up tissue, and cells (e.g., guard cells, egg cells, etc.)). In this regard, the transgenic plant or plants comprise a recombinant polynucleotide comprising a promoter of interest. The choice of promoter may include a constitutive promoter or a promoter with enhanced activity in a tissue capable of photosynthesis (also referred to herein as a “photosynthetic promoter” or a “photosynthetic tissue-enhanced promoter”) such as a leaf tissue or other green tissue. Examples of photosynthetic promoters include for example, an RBCS3 promoter, an RBCS4 promoter or others such as the At4g01060 (also referred to as “G682”) promoter, the latter regulating expression in a guard cell. The promoter regulates a polypeptide that is encoded by the recombinant polynucleotide or by a second (or target) recombinant polynucleotide (in which case expression of the polypeptide may be regulated by a trans-regulatory element). The promoter may also regulate expression of a polypeptide to an effective level of expression in a photosynthetic tissue, that is, to a level that, as a result of expression of the polypeptide to that level, improves photosynthetic resource use efficiency in a transgenic plant relative to a control plant. The recombinant polynucleotide may comprise the promoter and also encode the polypeptide or alternatively, the polynucleotide may comprise the promoter and drive expression of the polypeptide that is encoded by the second recombinant polynucleotide. In an exemplary embodiment, the polypeptide comprises a sequence listed in the sequence listing, or a sequence that is homologous, paralogous or orthologous to said polypeptide, being structurally-related to said polypeptide and having a function similar to said polypeptide as described herein. Expression of the polypeptide under the regulatory control of the constitutive or leaf-enhanced or photosynthetic tissue-enhanced promoter in the transgenic plant confers greater photosynthetic resource use efficiency to the transgenic plants, and may ultimately increase yield that may be obtained from the plants.

The instant description also pertains to methods for increasing photosynthetic resource use efficiency in, or increasing yield from, a plant or plants including the method conducted by growing a transgenic plant comprising and/or transformed with an expression cassette comprising the recombinant polynucleotide that comprises a constitutive promoter or a promoter expressed in photosynthetic tissue, which may be a leaf-enhanced or green tissue-enhanced promoter, such as for example, the RBCS3, RBCS4, At4g01060, or another photosynthetic tissue-enhanced promoter. Examples of photosynthetic tissue-enhanced promoters are found in the Sequence Listing or in Table 22. The promoter regulates expression of a polypeptide that comprises a polypeptide listed in the Sequence Listing. Recombinant polynucleotides encoding these clade polypeptides are described in the following paragraphs (a)-(c), and exemplary polypeptides within the clade are described in the following paragraphs (d)-(f) and are shown in the instant sequence alignments and Figures.

The recombinant polynucleotide that is introduced into a transgenic plant may encode a listed polypeptide sequence or encodes a polypeptide that is phylogenetically-related to a listed polypeptide sequence, including sequences that include:

(a) nucleic acid sequences that are at least 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to any of the listed polypeptides; and/or

(b) nucleic acid sequences that encode polypeptide sequences that are at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical in their amino acid sequences to the entire length to any of the listed polypeptides; and/or

(c) nucleic acid sequences that hybridize under stringent conditions (e.g., hybridization followed by one, by two, or by more than two wash steps of 6× saline-sodium citrate buffer (SSC) and 65° C. for ten to thirty minutes per step) to any of the listed polynucleotides.

The listed polypeptides and polypeptides member of their protein clade may include:

(d) polypeptide sequences encoded by the nucleic acid sequences of (a), (b) and/or (c); and/or

(e) polypeptide sequences that have at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65f %, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to any of the listed polypeptides, including SEQ ID NO: 2n, where n=1 to 241 (i.e., even integers 2, 4, 6, 8, . . . 482);

and/or at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65f %, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100 amino acid identity to a conserved domain of any of the listed polypeptides, including SEQ ID NO: 483 to 841; and/or

(f) polypeptide sequences that comprise a subsequence that are at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to any of the consensus sequences provided in the Sequence Listing, including SEQ ID NO: 842 to 861.

Expression of these polypeptides in the transgenic plant may confer increased photosynthetic resource use efficiency relative to a control plant. The transgenic plant may be selected for increased photosynthetic resource use efficiency or greater yield relative to the control plant. The transgenic plant may also be crossed with itself, a second plant from the same line as the transgenic plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed.

The instant description also pertains to methods for producing and selecting a crop plant with a greater yield than a control plant, the method comprising producing a transgenic plant by introducing into a target plant a recombinant polynucleotide that comprises a promoter, such as a leaf- or photosynthetic tissue-enhanced promoter that regulates a polypeptide encoded by the recombinant polynucleotide or a second recombinant polynucleotide, wherein the polypeptide comprises a polypeptide listed in the Sequence Listing, or a member of a clades of polypeptides phylogenetically related to a polypeptide listed in the Sequence Listing. A plurality of the transgenic plants is then grown, and a transgenic plant is selected that produces greater yield or has greater photosynthetic resource use efficiency than a control plant. The expression of the polypeptide in the selected transgenic plant confers the greater photosynthetic resource use efficiency and/or greater yield relative to the control plant. Optionally, the selected transgenic plant may be crossed with itself, a second plant from the same line as the transgenic plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed. A plurality of the selected transgenic plants will generally have greater cumulative canopy photosynthesis than the canopy photosynthesis of an identical number of the control plants.

The transgenic plant(s) described herein and produced by the instantly described methods may also possess one or more altered traits that result in greater photosynthetic resource use efficiency. The altered trait may include: increased photosynthetic capacity, increased photosynthetic rate, a decrease in leaf chlorophyll content, a decrease in percentage of nitrogen in leaf dry weight, increased leaf transpiration efficiency, an increase in resistance to water vapor diffusion from the leaf exerted by stomata, an increased rate of relaxation of photoprotective reactions operating in the light harvesting antennae, a decrease in the ratio of the carbon isotope ¹²C to ¹³C in above-ground biomass, and/or an increase in the total dry weight of above-ground plant material.

At least one advantage of greater photosynthetic resource use efficiency is that the transgenic plant, or a plurality of the transgenic plants, will have greater cumulative canopy photosynthesis than the canopy photosynthesis of an identical number of the control plants, or produce greater yield than an identical number of the control plants. A wide variety of transgenic plants are envisioned, including corn, wheat, rice, Setaria, Miscanthus, switchgrass, ryegrass, sugarcane, miscane, barley, sorghum, turfgrass, soy, cotton, canola, rapeseed, Crambe, Camelina, sugar beet, alfalfa, tomato, Eucalyptus, poplar, willow, pine, birch and other woody plants.

The instant description also pertains to expression vectors that comprise a recombinant polynucleotide that comprises a promoter expressed in photosynthetic tissue, for example, a constitutive promoter, or a leaf- or green tissue-enhanced promoter including the RBCS3, RBCS4, or At4g01060 promoters, or another photosynthetic tissue-enhanced promoter, for example, such a promoter found in the Sequence Listing or in Table 22, and a subsequence that encodes a polypeptide comprising a polypeptide sequence provided in the Sequence Listing or a member of the polypeptide clades of the polypeptide sequences listed in the Sequence Listing, or, alternatively, two expression constructs, one of which encodes a promoter such as a constitutive promoter, or a leaf-enhanced promoter or other photosynthetic tissue-enhanced promoter, and the second encodes a polypeptide sequence provided in the Sequence Listing or a member of the polypeptide clades of the polypeptide sequences listed in the Sequence Listing. In either instance, whether the polypeptide is encoded by the first or second expression constructs, the promoter regulates expression of the polypeptide by being responsible for production of cis- or trans-regulatory elements, respectively. In some embodiments, the expression vectors or cassettes comprise a promoter of the present application, and a gene of interest, wherein the promoter and the gene of interest do not link to each other under natural conditions, e.g., the linkage between the promoter and the gene of interest does not exist in nature.

The instant description is also directed to a method for producing a monocot plant with increased grain yield by providing a monocot plant cell or plant tissue with stably integrated, exogenous, recombinant polynucleotide comprising a promoter (for example, a constitutive, a non-constitutive, an inducible, a tissue-enhanced, or a photosynthetic tissue-enhanced promoter) that is functional in plant cells and that is operably linked to an exogenous or an endogenous nucleic acid sequence that encodes a listed polypeptide, that is expressed in a photosynthetic tissue of the transgenic plant to a level effective in conferring greater photosynthetic resource use efficiency relative to a control plant that does not contain the recombinant polynucleotide. A plant is generated from the plant cell or the plant tissue that comprises the recombinant polynucleotide, the plant is then grown and an increase in photosynthetic resource use efficiency or grain yield is measured relative to the control plant.

In the above paragraphs, the control plant may be exemplified by a plant of the same species as the plant comprising the recombinant polynucleotide, but the control plant does not comprise the recombinant polynucleotide that encodes a listed polypeptide of interest.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING AND DRAWINGS

The Sequence Listing provides exemplary polynucleotide and polypeptide sequences of the instant description. The traits associated with the use of the sequences are included in the Examples.

Incorporation of the Sequence Listing.

The Sequence Listing provides exemplary polynucleotide and polypeptide sequences. The copy of the Sequence Listing being submitted electronically with this patent application under 37 CFR § 1.821-1.825, is a read-only memory computer-readable file in ASCII text format. The Sequence Listing is named “MPS-0216P_ST25.txt”, the electronic file of the Sequence Listing was created on Oct. 2, 2013, and is (1,651,577 bytes in size (157 megabytes in size as measured in MS-WINDOWS). The Sequence Listing is herein incorporated by reference in its entirety.

In FIG. 1, a phylogenetic tree of ATMYB27 or AT3G53200 (also referred to as G1311) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. ATMYB27 (AT3G53200.1) appears in the rounded rectangle. An ancestral sequence of ATMYB27 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 1. ATMYB27 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by AT3G53200.1 and GSVIVT01033670001_VITVI.

FIGS. 2A-2D show an alignment of ATMYB27 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second Myb domains appear in boxes in FIGS. 2A-2B and FIG. 2B, respectively (for which the consensus sequences are SEQ ID NOs 842 and 843).

FIG. 3: Plot showing increased light saturated photosynthesis (A_(sat)) over a range of leaf sub-stomatal CO₂ concentration (C_(i)) in three ATMYB27 overexpression lines, compared to a control line. Data was collected over a range of C_(i) over which the activity of Rubisco is known to limit A_(sat). The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line.

Legend for FIG. 3:

Control

□ Line 1

Δ Line 2

X Line 4

⋄ Line 5

◯ Line 6

FIG. 4: Plot showing increased light saturated photosynthesis (A_(sat)) over a range of leaf sub-stomatal CO₂ concentration (C_(i)) in four ATMYB27 overexpression lines, compared to a control line. Data was collected over a range of C_(i) over which the capacity to regenerate RuBP is known to limit A_(sat). The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line.

Legend for FIG. 4:

Control

□ Line 1

Δ Line 2

X Line 4

⋄ Line 5

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In FIGS. 5A and 5B, a phylogenetic tree of RPB45A or AT5G54900 (also referred to as G1940) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. RPB45A (AT5G54900.1) appears in the rounded rectangle in FIG. 5B. An ancestral sequence of RPB45A and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 5B. RPB45A clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi5g22410.1_BRADI and Solyc03g031720.2.1_SOLLY.

FIGS. 6A-6AF show an alignment of RPB45A and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first, second, and third RNA Recognition Motif (RRM) domains appear in boxes in FIGS. 6I-6N, FIGS. 6M-6R, and 6S-6X, respectively (for which the consensus sequences are SEQ ID NOs 844, 845 and 846, respectively).

In FIG. 7, a phylogenetic tree of TCP6 or AT5G41030 (also referred to as G1936) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. TCP6 (AT5G41030.1) appears in the rounded rectangle. An ancestral sequence of TCP6 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 7. TCP6 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi2g59240.1_BRADI and Solyc02g094290.1.1_SOLLY.

FIGS. 8A-8L show an alignment of TCP6 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved TCP domain appears in boxes in FIGS. 8C-8E (for which the consensus sequence is SEQ ID NO 847).

In FIG. 9, a phylogenetic tree of PIL1 or AT2G46970 (also referred to as G1649) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. The PIL1 clade members appear in the large box with the solid line boundary. PIL1 (AT2G46970.1) appears in the rounded rectangle. An ancestral sequence of PIL1 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 9. PIL1 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by AT2G46970.1_ARATH and POPTR_0014s10700.1_POPTR.

FIGS. 10A-10F show an alignment of PIL1 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved bHLH domain appears in boxes in FIGS. 10D-10E (for which the consensus sequence is SEQ ID NO 848).

In FIG. 11, a phylogenetic tree of PCL1 or AT3G46640 (also referred to as G2741) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. PCL1 (AT3G46640.3) appears in the rounded rectangle. An ancestral sequence of PCL1 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 11. PCL1 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi2g62067.1_BRADI and GSVIVT01024916001_VITVI.

FIGS. 12A-12N show an alignment of PCL1 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved SANT (aka Myb-related or GARP) domain appears in boxes in FIGS. 12H-12I (for which the consensus sequence is SEQ ID NO 849).

FIG. 13: Plot showing increased light saturated photosynthesis (A_(sat)) over a range of leaf sub-stomatal CO₂ concentration (C_(i)) in four PCL1 overexpression lines, compared to a control line. Data was collected over a range of C_(i) where the activity of Rubisco is known to limit A_(sat). The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least seven replicate plants for each line.

Legend for FIG. 13:

Control

□ Line 1

Δ Line 2

X Line 3

⋄ Line 4

◯ Line 5

In FIG. 14, a phylogenetic tree of GTL1 or AT1G33240 (also referred to as G634) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. GTL1 (AT1G33240.1) appears in the rounded rectangle. An ancestral sequence of GTL1 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 14. GTL1 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi5g17150.1_BRADI and POPTR_0005s21420.1_POPTR.

FIGS. 15A-15X show an alignment of GTL1 and representative clade-related proteins. The sequence denoted G634_P77591 was the splice variant of GTL1 that was expressed in plants. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second trihelix (aka GT or Myb/SANT-related) domains appear in boxes in FIGS. 15C-15E and FIGS. 150-15Q, respectively (for which the consensus sequences are SEQ ID NOs 850 and 851).

In FIG. 16, a phylogenetic tree of DREB2H or AT2G40350 (also referred to as G1755) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. DREB2H (AT2G40350.1) appears in the rounded rectangle. An ancestral sequence of DREB2H and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 16. DREB2H clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi2g04000.1_BRADI and Solyc06g050520.1.1_SOLLY.

FIGS. 17A-17N show an alignment of DREB2H and representative clade-related proteins. The sequence denoted G1755_P4407 was the sequence of the DREB2H clone expressed in plants. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved AP2 domain appears in boxes in FIGS. 17E-17F (for which the consensus sequence is SEQ ID NO 852).

In FIG. 18, a phylogenetic tree of ERF087 or AT1G28160 (also referred to as G2292) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. ERF087 (AT1G28160.1) appears in the rounded rectangle. An ancestral sequence of ERF087 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 18. ERF087 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi3g44470.1_BRADI and Glyma16g05070.1_GLYMA.

FIGS. 19A-19J show an alignment of ERF087 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved AP2 domain appears in boxes in FIGS. 19C-19D, respectively (for which the consensus sequence is SEQ ID NO 853).

FIG. 20: Non-photochemical quenching (NPQ) dynamics at 22° C. Plot showing decreased NPQ in multiple ERF087 overexpression lines, during short term acclimation to high light. NPQ was calculated from an initial measurement of maximal, dark adapted fluorescence (F_(m)) and subsequent measurements of fluorescence made under varying incident light (F_(m)), as NPQ=(F_(m)/F′_(m))−1. During the nine minute assay F′_(m) was measured at 30 second intervals: initially after exposure to 700 μmol PAR m⁻² s⁻¹ beginning immediately after F_(m) was measured; then, after a decrease to 0 μmol PAR m⁻² s⁻¹ after 3 minutes; then, after an increase to 2000 μmol PAR m⁻² s⁻¹ after 4 minutes. All symbols are the mean±1 standard error of measurements made on at least five replicate leaves for a given line (‘PAR’ refers to photosynthetically active radiation).

Legend for FIG. 20:

Control

□ Line 1

⋄ Line 2

X Line 3

◯ Line 4

Δ Line 5

+ Line 6

FIG. 21: Non-photochemical quenching (NPQ) dynamics at 35° C. Plot showing decreased NPQ in multiple ERF087 overexpression lines, during short term acclimation to high light. NPQ was calculated from an initial measurement of maximal, dark adapted fluorescence (F_(m)) and subsequent measurements of fluorescence made under varying incident light (F′_(m)), as NPQ=(F_(m)/F′_(m))−1. During the nine minute assay F′_(m) was measured at 30 second intervals: initially after exposure to 700 μmol PAR m⁻² s⁻¹ beginning immediately after F_(m) was measured; then, after a decrease to 0 μmol PAR m⁻² s⁻¹ after 3 minutes; then, after an increase to 2000 μmol PAR m⁻² s⁻¹ after 4 minutes. All symbols are the mean±1 standard error of measurements made on at least five replicate leaves for a given line.

Legend for FIG. 21:

Control

□ Line 1

⋄ Line 2

X Line 3

◯ Line 4

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+ Line 6

In FIG. 22, a phylogenetic tree of BBX18 or AT2G21320 (also referred to as G1881) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. BBX18 (AT2G21320.1) appears in the rounded rectangle. An ancestral sequence of BBX18 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 22. BBX18 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi4g35950.1_BRADI and Solyc02g084420.2.1_SOLLY.

FIGS. 23A-23G show an alignment of BBX18 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved first and second B-box domains appear in boxes in FIGS. 23A-23B and FIGS. 23B-23C, respectively (for which the consensus sequences are SEQ ID NOs 854 and 855).

FIG. 24: Plot showing increased light saturated photosynthesis (A_(sat)) over a range of leaf sub-stomatal CO₂ concentration (C_(i)) in three BBX18 overexpression lines, compared to a control line. Data was collected over a range of C_(i), from low, where the activity of Rubisco is known to limit A_(sat), to high, where the capacity to regenerate RuBP limits A_(sat). The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least seven replicate plants for each line.

Legend for FIG. 24:

Control

Δ Line 4

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□ Line 6

In FIG. 25, a phylogenetic tree of bHLH60 or AT3G57800 (also referred to as G2144) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. bHLH60 (AT3G57800.1) appears in the rounded rectangle. An ancestral sequence of bHLH60 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 25. bHLH60 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradilg35990.1_BRADI and Solyc10g079070.1.1_SOLLY.

FIGS. 26A-26N show an alignment of bHLH60 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved bHLH domain appears in boxes FIGS. 26H-261 (for which the consensus sequence is SEQ ID NO 856).

In FIG. 27, a phylogenetic tree of NF-YC6 or AT5G50480 (also referred to as G1820) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. NF-YC6 (AT5G50480.1) appears in the rounded rectangle. An ancestral sequence of NF-YC6 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 27. NF-YC6 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi3g17790.1_BRADI and Solyc03g111450.1.1_SOLLY.

FIGS. 28A-28T show an alignment of NF-YC6 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved NF-Y/histone-like domain appears in boxes in FIGS. 28J-28L (for which the consensus sequence is SEQ ID NO 857).

In FIG. 29, a phylogenetic tree of bHLH121 or AT3G19860 (also referred to as G782) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. bHLH121 (AT3G19860.2) appears in the rounded rectangle. An ancestral sequence of bHLH121 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 29. bHLH121 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi3g11520.1_BRADI and SolycOlg111130.2.1_SOLLY.

FIGS. 30A-30K show an alignment of bHLH121 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved bHLH domains appear in boxes in FIGS. 30B-30D, respectively (SEQ ID NO 858). A distinct putative leucine zipper motif and its consensus sequence that is found with these clade members comprising is found in FIG. 30D (SEQ ID NO: 859), enclosed in a dotted line box.

FIG. 31: Plot showing increased light saturated photosynthesis (A_(sat)) over a range of leaf sub-stomatal CO₂ concentration (C_(i)) in four out of five bHLH121 overexpression lines, compared to a control line. Data was collected over a range of C_(i) over which the capacity to regenerate RuBP is known to limit A_(sat). The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least five replicate plants for each line.

Legend for FIG. 31:

Control

+ Line 1

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∘ Line 4

X Line 5

In FIG. 32, a phylogenetic tree of BBX26 or AT1G60250 (also referred to as G1486) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. BBX26 (AT1G60250) appears in the rounded rectangle. An ancestral sequence of BBX26 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 32. BBX26 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by AT3G53200 ARATH and Solyc04007470.2 SOLLY.

FIGS. 33A-33E show an alignment of BBX26 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved B-box domain appears in boxes in FIG. 33A (for which the consensus sequence is SEQ ID NO 860).

FIG. 34: Plot showing increased light saturated photosynthesis (A_(sat)) over a range of leaf sub-stomatal CO₂ concentration (C_(i)) in four BBX26 overexpression lines, compared to a control line. Data was collected over a range of C_(i) over which the capacity to regenerate RuBP is known to limit A_(sat). The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least six replicate plants for each line.

Legend for FIG. 34:

Control

* Line 1

+ Line 2

◯ Line 3

Δ Line 4

□ Line 5

In FIGS. 35A and 35B, a phylogenetic tree of PMT24 or AT1G29470 (also referred to as G837) clade members and related full length proteins were constructed using TreeBeST (Ruan et al., 2008. Nucleic Acids Res. 36 (suppl. 1): D735-D740) using the best command to identify the best tree from maximum likelihood and neighbor joining methods. PMT24 (AT1G29470.1) appears in the rounded rectangle in FIG. 35B. An ancestral sequence of PMT24 and closely-related sequences is represented by the node of the tree indicated by the arrow “A” in FIG. 35B. PMT24 clade members are considered those proteins that descended from ancestral sequence “A”, including the exemplary sequences shown in this figure that are bounded by Bradi2g57087.1_BRADI and GSVIVT01026451001_VITVI.

FIGS. 36A-36X show an alignment of PMT24 and representative clade-related proteins. The alignment was generated with MUSCLE (3.8) with default parameters. SEQ ID NOs: appear in parentheses after each Gene Identifier (GID). The conserved putative methyltransferase domain appears in boxes in FIGS. 36M-36S (for which the consensus sequence is SEQ ID NO 861).

FIG. 37: Plot showing increased light saturated photosynthesis (A_(sat)) over a range of leaf sub-stomatal CO₂ concentration (C_(i)) in four out of five PMT24 overexpression lines, compared to a control line. Data was collected over a range of C_(i) over which the capacity to regenerate RuBP is known to limit A_(sat). The solid line shown is a regression fitted to the data for the control line only. All data are the means±1 standard error for data collected on at least five replicate plants for each line.

Legend for FIG. 37:

Control

□ Line 3

◯ Line 4

X Line 5

Δ Line 6

* Line 7

DETAILED DESCRIPTION

The present description relates to polynucleotides and polypeptides for modifying phenotypes of plants, particularly those associated with increased photosynthetic resource use efficiency and increased yield with respect to a control plant. Throughout this disclosure, various information sources are referred to and/or are specifically incorporated. The information sources include scientific journal articles, patent documents, textbooks, and internet entries. While the reference to these information sources clearly indicates that they can be used by one of skill in the art, each and every one of the information sources cited herein are specifically incorporated in their entirety, whether or not a specific mention of “incorporation by reference” is noted. The contents and teachings of each and every one of the information sources can be relied on and used to make and use embodiments of the instant description.

As used herein and in the appended claims, the singular forms “a”, “an”, and “the” include the plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a host cell” includes a plurality of such host cells, and a reference to “a plant” is a reference to one or more plants, and so forth.

A “recombinant polynucleotide” is a polynucleotide that is not in its native state, e.g., the polynucleotide comprises a nucleotide sequence not found in nature, or the polynucleotide is in a context other than that in which it is naturally found, e.g., separated from nucleotide sequences with which it typically is in proximity in nature, or adjacent (or contiguous with) nucleotide sequences with which it typically is not in proximity. For example, the sequence at issue can be cloned into a vector, or otherwise recombined with one or more additional nucleic acid.

A “polypeptide” is an amino acid sequence comprising a plurality of consecutive polymerized amino acid residues e.g., at least about 15 consecutive polymerized amino acid residues. In many instances, a polypeptide comprises a polymerized amino acid residue sequence that is a regulatory polypeptide or a domain or portion or fragment thereof. Additionally, the polypeptide may comprise: (i) a localization domain; (ii) an activation domain; (iii) a repression domain; (iv) an oligomerization domain; (v) a protein-protein interaction domain; (vi) a DNA-binding domain; or the like. The polypeptide optionally comprises modified amino acid residues, naturally occurring amino acid residues not encoded by a codon, or non-naturally occurring amino acid residues.

“Protein” refers to an amino acid sequence, oligopeptide, peptide, polypeptide or portions thereof whether naturally occurring or synthetic.

In the instant description, “exogenous” refers to a heterologous nucleic acid or polypeptide that may not be naturally expressed in a plant of interest. Exogenous nucleic acids may be introduced into a plant in a stable or transient manner via, for example, transformation or breeding, and may thus serve to produce in planta a homologous RNA molecule and an encoded and functional polypeptide. Exogenous nucleic acids and polypeptides introduced thusly may comprise sequences that are wholly or partially identical or homologous to sequences that naturally occur in (i.e., are endogenous with respect to) the plant.

A “recombinant polypeptide” is a polypeptide produced by translation of a recombinant polynucleotide. A “synthetic polypeptide” is a polypeptide created by consecutive polymerization of isolated amino acid residues using methods well known in the art. An “isolated polypeptide,” whether a naturally occurring or a recombinant polypeptide, is more enriched in (or out of) a cell than the polypeptide in its natural state in a wild-type cell, e.g., more than about 5% enriched, more than about 10% enriched, or more than about 20%, or more than about 50%, or more, enriched, i.e., alternatively denoted: 105%, 110%, 120%, 150% or more, enriched relative to wild type standardized at 100%. Such an enrichment is not the result of a natural response of a wild-type plant. Alternatively, or additionally, the isolated polypeptide is separated from other cellular components with which it is typically associated, e.g., by any of the various protein purification methods herein.

“Identity” or “similarity” refers to sequence similarity between two polynucleotide sequences or between two polypeptide sequences, with identity being a more strict comparison. The phrases “percent identity” and “% identity” refer to the percentage of sequence similarity found in a comparison of two or more polynucleotide sequences or two or more polypeptide sequences. “Sequence similarity” refers to the percent similarity in base pair sequence (as determined by any suitable method) between two or more polynucleotide sequences. Two or more sequences can be anywhere from 0-100% similar or identical, or any integer value between 0-100%. Identity or similarity can be determined by comparing a position in each sequence that may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same nucleotide base or amino acid, then the molecules are identical at that position. A degree of similarity or identity between polyBLAST nucleotide sequences is a function of the number of identical, matching or corresponding nucleotides at positions shared by the polynucleotide sequences. A degree of identity of polypeptide sequences is a function of the number of identical amino acids at corresponding positions shared by the polypeptide sequences. A degree of homology or similarity of polypeptide sequences is a function of the number of amino acids at corresponding positions shared by the polypeptide sequences. The fraction or percentage of components in common is related to the homology or identity between the sequences. Alignments such as those of FIG. 2A-2E may be used to identify conserved domains and relatedness within these domains. An alignment may suitably be determined by means of computer programs known in the art, such as MACVECTOR software, (1999; Accelrys, Inc., San Diego, Calif.).

“Homologous sequences” refers to polynucleotide or polypeptide sequences that are similar due to common ancestry and sequence conservation. The terms “ortholog” and “paralog” are defined below in the section entitled “Orthologs and Paralogs”. In brief, orthologs and paralogs are evolutionarily related genes that have similar sequences and functions. Orthologs are structurally related genes in different species that are derived by a speciation event. Paralogs are structurally related genes within a single species that are derived by a duplication event.

“Functional homologs” are polynucleotide or polypeptide sequences, including orthologs and paralogs, that are similar due to common ancestry and sequence conservation and have identical or similar function at the catalytic, cellular, or organismal levels. The presently disclosed polypeptides, clade members and phylogenetically related sequences are “functionally-related and/or closely-related” by having descended from common ancestral sequences, and/or by being sufficiently similar to the sequences and domains listed in the instant Tables and Sequence Listing that they confer the same function to plants of increased photosynthetic resource use efficiency, increased yield, increased grain yield, increased light use efficiency, increased photosynthetic capacity, increased photosynthetic rate, greater vigor, and/or greater biomass as compared to a control plant.

Functionally-related and/or closely-related polypeptides may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed closely-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.

“Conserved domains” are recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis. A “conserved domain” or “conserved region” as used herein refers to a region in heterologous polynucleotide or polypeptide sequences where there is a relatively high degree of sequence identity between the distinct sequences. Conserved domains contain conserved sequence patterns or motifs that allow for their detection in, and identification and characterization of, polypeptide sequences. A Myb domain is an example of a conserved domain.

A transgenic plant is expected to have improved or increased photosynthetic resource use efficiency relative to a control plant when the transgenic plant is transformed with a recombinant polynucleotide encoding any of the listed polypeptide sequences or polypeptide found in polypeptide clade of any of the listed polypeptide sequences, or when the transgenic plant contains or expresses a listed polypeptide or a member of any of the same polypeptide clades sequence in which the listed polypeptides may be found.

The terms “highly stringent” or “highly stringent condition” refer to conditions that permit hybridization of DNA strands whose sequences are highly complementary, wherein these same conditions exclude hybridization of significantly mismatched DNAs. Polynucleotide sequences capable of hybridizing under stringent conditions with the polynucleotides of the present description may be, for example, variants of the disclosed polynucleotide sequences, including allelic or splice variants, or sequences that encode orthologs or paralogs of presently disclosed polypeptides. Nucleic acid hybridization methods are disclosed in detail by Kashima et al., 1985. Nature 313: 402-404; Sambrook et al., 1989. Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., and by Haymes et al., 1985. Nucleic Acid Hybridization: A Practical Approach, IRL Press, Washington, D.C., which references are incorporated herein by reference.

In general, stringency is determined by the temperature, ionic strength, and concentration of denaturing agents (e.g., formamide) used in a hybridization and washing procedure (for a more detailed description of establishing and determining stringency, see the section “Identifying Polynucleotides or Nucleic Acids by Hybridization”, below). The degree to which two nucleic acids hybridize under various conditions of stringency is correlated with the extent of their similarity. Thus, similar nucleic acid sequences from a variety of sources, such as within a plant's genome (as in the case of paralogs) or from another plant (as in the case of orthologs) that may perform similar functions can be isolated on the basis of their ability to hybridize with known related polynucleotide sequences. Numerous variations are possible in the conditions and means by which nucleic acid hybridization can be performed to isolate related polynucleotide sequences having similarity to sequences known in the art and are not limited to those explicitly disclosed herein. Such an approach may be used to isolate polynucleotide sequences having various degrees of similarity with disclosed polynucleotide sequences, such as, for example, encoded regulatory polypeptides listed in the Sequence Listing, or polypeptides that are phylogenetically related to the polypeptides listed in the Sequence Listing.

“Fragment”, with respect to a polynucleotide, refers to a clone or any part of a polynucleotide molecule that retains a usable, functional characteristic. Useful fragments include oligonucleotides and polynucleotides that may be used in hybridization or amplification technologies or in the regulation of replication, transcription or translation. A “polynucleotide fragment” refers to any subsequence of a polynucleotide, typically, of at least about nine consecutive nucleotides, preferably at least about 30 nucleotides, more preferably at least about 50 nucleotides, of any of the sequences provided herein. Exemplary polynucleotide fragments are the first sixty consecutive nucleotides of the polynucleotides listed in the Sequence Listing. Exemplary fragments also include fragments that comprise a region that encodes an conserved domain of a polypeptide. Exemplary fragments also include fragments that comprise a conserved domain of a polypeptide. Exemplary fragments include fragments that comprise an conserved domain of a polypeptide, for example, any of the domains listed in in the instant Tables or in the Sequence Listing.

Fragments may also include subsequences of polypeptides and protein molecules, or a subsequence of the polypeptide. Fragments may have uses in that they may have antigenic potential. In some cases, the fragment or domain is a subsequence of the polypeptide which performs at least one biological function of the intact polypeptide in substantially the same manner, or to a similar extent, as does the intact polypeptide. For example, a polypeptide fragment can comprise a recognizable structural motif or functional domain such as a DNA-binding site or domain that binds to a DNA promoter region, an activation domain, or a domain for protein-protein interactions, and may initiate transcription. Fragments can vary in size from as few as three amino acid residues to the full length of the intact polypeptide, but are preferably at least about 30 amino acid residues in length and more preferably at least about 60 amino acid residues in length.

Fragments may also refer to a functional fragment of a promoter region. For example, a recombinant polynucleotide capable of modulating transcription in a plant may comprise a nucleic acid sequence with similarity to, or a percentage identity to, a promoter region exemplified by a promoter sequence provided in the Sequence Listing (also see promoters listed in Example II), a fragment thereof, or a complement thereof, wherein the nucleic acid sequence, or the fragment thereof, or the complement thereof, regulates expression of a polypeptide in a plant cell.

The term “plant” includes whole plants, shoot vegetative organs/structures (for example, leaves, stems and tubers), roots, flowers and floral organs/structures (for example, bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (for example, vascular tissue, ground tissue, and the like), pulped, pureed, ground-up, macerated or broken-up tissue, and cells (for example, guard cells, egg cells, and the like), and progeny of same. The class of the plants that can be transformed using the methods provided of the instant description is generally as broad as the class of higher and lower plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), gymnosperms, ferns, horsetails, psilophytes, lycophytes, and bryophytes. These plant parts, organs, structures, cells, tissue, or progeny may contain a recombinant polynucleotide of interest, such as one that comprises a described or listed polynucleotide or one that encodes a described or listed polypeptide or a polypeptide that is phylogenetically-related to a listed polypeptide, and is thus a member of the same polypeptide clade.

A “control plant” as used in the present description refers to a plant cell, seed, plant component, plant tissue, plant organ or whole plant used to compare against transgenic or genetically modified plant for the purpose of identifying an enhanced phenotype in the transgenic or genetically modified plant. A control plant may in some cases be a transgenic plant line that comprises an empty vector or marker gene, but does not contain the recombinant polynucleotide of the present description that is expressed in the transgenic or genetically modified plant being evaluated. In general, a control plant is a plant of the same line or variety as the transgenic or genetically modified plant being tested. A suitable control plant would include a genetically unaltered or non-transgenic plant of the parental line used to generate a transgenic plant herein.

A “transgenic plant” refers to a plant that contains genetic material not found in a wild-type plant of the same species, variety or cultivar. The genetic material may include a transgene, an insertional mutagenesis event (such as by transposon or T-DNA insertional mutagenesis), an activation tagging sequence, a mutated sequence, a homologous recombination event or a sequence modified by chimeraplasty. Typically, the foreign genetic material has been introduced into the plant by human manipulation, but any method can be used as one of skill in the art recognizes.

A transgenic line or transgenic plant line refers to the progeny plant or plants deriving from the stable integration of heterologous genetic material into a specific location or locations within the genome of the original transformed cell.

A transgenic plant may contain an expression vector or cassette. The expression vector or cassette typically comprises a polypeptide-encoding sequence operably linked (i.e., under regulatory control of) to appropriate inducible, tissue-enhanced, tissue-specific, or constitutive regulatory sequences that allow for the controlled expression of the polypeptide. The expression vector or cassette can be introduced into a plant by transformation or by breeding after transformation of a parent plant. A plant refers to a whole plant as well as to a plant part, such as seed, fruit, leaf, or root, plant tissue, plant cells or any other plant material, e.g., a plant explant, as well as to progeny thereof, and to in vitro systems that mimic biochemical or cellular components or processes in a cell. In some other embodiments, the expression vectors or cassettes do not occur naturally. In some embodiments, the expression vectors or cassettes comprise a promoter of the present application, and a gene of interest, wherein the promoter and the gene of interest do not link to each other under natural conditions, e.g., the linkage between the promoter and the gene of interest does not exist in nature. For example, in some embodiments, the promoter and the gene of interest are derived from a same plant species, but are not linked to each other under natural conditions. In some embodiments, the promoter and the gene of interest are derived from two different species, e.g., the promoter and the gene of interest are heterologous to each other. In some embodiments, the gene of interest is derived from a different plant species, a bacteria species, a fungal species, a viral species, an algae species, or an animal species. In some embodiments, the expression vectors or cassettes comprise synthetic sequences.

“Germplasm” refers to a genetic material or a collection of genetic resources for an organism from an individual plant, a group of related individual plants (for example, a plant line, a plant variety or a plant family), or a clone derived from a plant line, plant variety, plant species, or plant culture.

A constitutive promoter is active under most environmental conditions, and in most plant parts. Regulation of protein expression in a constitutive manner refers to the control of expression of a gene and/or its encoded protein in all tissues regardless of the surrounding environment or development stage of the plant.

Alternatively, expression of the disclosed or listed polypeptides may be under the regulatory control of a promoter that is not a constitutive promoter. For example, tissue-enhanced (also referred to as tissue-preferred), tissue-specific, cell type-specific, and inducible promoters constitute non-constitutive promoters; that is, these promoters do not regulate protein expression in a constitutive manner. Tissue-enhanced or tissue-preferred promoters facilitate expression of a gene and/or its encoded protein in specific tissue(s) and generally, although perhaps not completely, do not express the gene and/or protein in all other tissues of the plant, or do so to a much lesser extent. Promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as xylem, leaves, roots, or seeds. Such promoters are examples of tissue-enhanced or tissue-preferred promoters (see U.S. Pat. No. 7,365,186). Tissue-specific promoters generally confine transgene expression to a single plant part, tissue or cell-type, although many such promoters are not perfectly restricted in their expression and their regulatory control is more properly described as being “tissue-enhanced” or “tissue-preferred”. Tissue-enhanced promoters primarily regulate transgene expression in a limited number of plant parts, tissues or cell-types and cause the expression of proteins to be overwhelming restricted to a few particular tissues, plant parts, or cell types. An example of a tissue-enhanced promoter is a “photosynthetic tissue-enhanced promoter”, for which the promoter preferentially regulates gene or protein expression in photosynthetic tissues (e.g., leaves, cotyledons, stems, etc.). Tissue-enhanced promoters can be found upstream and operatively linked to DNA sequences normally transcribed in higher levels in certain plant tissues or specifically in certain plant tissues, respectively. “Cell-enhanced”, “tissue-enhanced”, or “tissue-specific” regulation thus refer to the control of gene or protein expression, for example, by a promoter that drives expression that is not necessarily totally restricted to a single type of cell or tissue, but where expression is elevated in particular cells or tissues to a greater extent than in other cells or tissues within the organism, and in the case of tissue-specific regulation, in a manner that is primarily elevated in a specific tissue. Tissue-enhanced or preferred promoters have been described in, for example, U.S. Pat. No. 7,365,186, or U.S. Pat. No. 7,619,133.

Another example of a promoter that is not a constitutive promoter is a “condition-enhanced” promoter, the latter term referring to a promoter that activates a gene in response to a particular environmental stimulus. This may include, for example, an abiotic stress, infection caused by a pathogen, light treatment, etc., and a condition-enhanced promoter drives expression in a unique pattern which may include expression in specific cell and/or tissue types within the organism (as opposed to a constitutive expression pattern in all cell types of an organism at all times).

“Wild type” or “wild-type”, as used herein, refers to a plant cell, seed, plant component, plant tissue, plant organ or whole plant that has not been genetically modified or treated in an experimental sense. Wild-type cells, seed, components, tissue, organs or whole plants may be used as controls to compare levels of expression and the extent and nature of trait modification with cells, tissue or plants of the same species in which a polypeptide's expression is altered, e.g., in that it has been knocked out, overexpressed, or ectopically expressed.

When two or more plants have “similar morphologies”, “substantially similar morphologies”, “a morphology that is substantially similar”, or are “morphologically similar”, the plants have comparable forms or appearances, including analogous features such as overall dimensions, height, width, mass, root mass, shape, glossiness, color, stem diameter, leaf size, leaf dimension, leaf density, internode distance, branching, root branching, number and form of inflorescences, and other macroscopic characteristics at a particular stage of growth. It may be difficult to distinguish two plants that are genotypically distinct but morphologically similar based on morphological characteristics alone. If the plants are morphologically similar at all stages of growth, they are also “developmentally similar”.

With regard to gene knockouts as used herein, the term “knockout” (KO) refers to a plant or plant cell having a disruption in at least one gene in the plant or cell, where the disruption results in a reduced expression or activity of the polypeptide encoded by that gene compared to a control cell. The knockout can be the result of, for example, genomic disruptions, including transposons, tilling, and homologous recombination, antisense constructs, sense constructs, RNA silencing constructs, or RNA interference. A T-DNA insertion within a gene is an example of a genotypic alteration that may abolish expression of that gene.

“Ectopic expression” or “altered expression” in reference to a polynucleotide indicates that the pattern of expression in, e.g., a transgenic plant or plant tissue, is different from the expression pattern in a wild-type plant or a reference plant of the same species. The pattern of expression may also be compared with a reference expression pattern in a wild-type plant of the same species. For example, the polynucleotide or polypeptide is expressed in a cell or tissue type other than a cell or tissue type in which the sequence is expressed in the wild-type plant, or by expression at a time other than at the time the sequence is expressed in the wild-type plant, or by a response to different inducible agents, such as hormones or environmental signals, or at different expression levels (either higher or lower) compared with those found in a wild-type plant. The term also refers to altered expression patterns that are produced by lowering the levels of expression to below the detection level or completely abolishing expression. The resulting expression pattern can be transient or stable, constitutive or inducible. In reference to a polypeptide, the term “ectopic expression or altered expression” further may relate to altered activity levels resulting from the interactions of the polypeptides with exogenous or endogenous modulators or from interactions with factors or as a result of the chemical modification of the polypeptides.

The term “overexpression” as used herein refers to a greater expression level of a gene in a plant, plant cell or plant tissue, compared to expression of that gene in a wild-type plant, cell or tissue, at any developmental or temporal stage. Overexpression can occur when, for example, the genes encoding one or more polypeptides are under the control of a strong promoter (e.g., the cauliflower mosaic virus 35S transcription initiation region). Overexpression may also be achieved by placing a gene of interest under the control of an inducible or tissue specific promoter, or may be achieved through integration of transposons or engineered T-DNA molecules into regulatory regions of a target gene. Other means for inducing overexpression may include making targeted changes in a gene's native promoter, e.g. through elimination of negative regulatory sequences or engineering positive regulatory sequences, though the use of targeted nuclease activity (such as zinc finger nucleases or TAL effector nucleases) for genome editing. Elimination of micro-RNA binding sites in a gene's transcript may also result in overexpression of that gene. Additionally, a gene may be overexpressed by creating an artificial transcriptional activator targeted to bind specifically to its promoter sequences, comprising an engineered sequence-specific DNA binding domain such as a zinc finger protein or TAL effector protein fused to a transcriptional activation domain. Thus, overexpression may occur throughout a plant, in specific tissues of the plant, or in the presence or absence of particular environmental signals, depending on the promoter or overexpression approach used.

Overexpression may take place in plant cells normally lacking expression of polypeptides functionally equivalent or identical to the present polypeptides. Overexpression may also occur in plant cells where endogenous expression of the present polypeptides or functionally equivalent molecules normally occurs, but such normal expression is at a lower level. Overexpression thus results in a greater than normal production, or “overproduction” of the polypeptide in the plant, cell or tissue.

“Photosynthetic resource-use efficiency” is defined as the rate of photosynthesis achieved per unit use of a given resource. Consequently, increases in photosynthesis relative to the use of a given resource will improve photosynthetic resource-use efficiency. Photosynthesis is constrained by the availability of various resources, including light, water and nitrogen. Improving the efficiency with which photosynthesis makes use of light, water and nitrogen is a means for increasing plant productivity, crop growth, and yield. For the purposes of comparing a plant of interest to a reference or control plant, the ratio of photosynthesis to use of a given resource is often determined for a fixed unit of leaf area. Examples of increased photosynthetic resource-use efficiency would be an increase in the ratio of the rate of photosynthesis for a given leaf relative to, for example, the rate of transpiration from the same leaf area, nitrogen or chlorophyll invested in that leaf area, or light absorbed by that same leaf area. Increased photosynthetic resource use efficiency may result from increased photosynthetic rate, photosynthetic capacity, a decrease in leaf chlorophyll content, a decrease in percentage of nitrogen in leaf dry weight, increased transpiration efficiency, an increase in resistance to water vapor diffusion exerted by leaf stomata, an increased rate of relaxation of photoprotective reactions operating in the light harvesting antennae, a decrease in the ratio of the carbon isotope ¹²C to ¹³C in above-ground biomass, and/or an increase in the total dry weight of above-ground plant material.

“Photosynthetic rate” refers to the rate of photosynthesis achieved by a leaf, and is typically expressed relative to a unit of leaf area. The photosynthetic rate at any given time results from the photosynthetic capacity of the leaf (see below) and the biotic or abiotic environmental constraints prevailing at that time.

“Photosynthetic capacity” refers to the capacity for photosynthesis per unit leaf area and is set by the leafs investment in the components of the photosynthetic apparatus. Key components, among many, would be the pigments and proteins required to regulate light absorption and transduction of light energy to the photosynthetic reaction centers, and the enzymes required to operate the C3 and C4 dark reactions of photosynthesis. Increasing photosynthetic capacity is seen as an important means of increasing leaf and crop-canopy photosynthesis, and crop yield.

“Rubisco (ribulose-1,5-bisphosphate carboxylase oxygenase) activity” refers to the activation state of Rubisco, the most abundant protein in the chloroplast and a key limitation to C3 photosynthesis. Increasing Rubisco activity by: increasing the amount of Rubisco in the chloroplast; impacting any combination of specific reactions that regulate Rubisco activity; or increasing the concentration of CO₂ in the chloroplast, is seen as an important means to improving C3 leaf and crop-canopy photosynthesis and crop yield.

The “capacity for RuBP (ribulose-1,5-bisphosphate) regeneration” refers to the rate at which RuBP, a key photosynthetic substrate is regenerated in the Calvin cycle. Increasing the capacity for RuBP regeneration by increasing the activity of enzymes in the regenerative phase of the Calvin cycle is seen as an important means to improving C3 leaf and crop-canopy photosynthesis and crop yield that will become progressively more important as atmospheric CO₂ concentrations continue to rise.

“Leaf chlorophyll content” refers to the chlorophyll content of the leaf expressed either per unit leaf area or unit weight. Sun leaves in the upper part of crop canopies are thought to have higher leaf chlorophyll content than is required for photosynthesis. The consequence is that these leaves: invest more nitrogen in chlorophyll than is required for photosynthesis; are prone to photodamage associated with absorbing more light energy than can be dissipated via photosynthesis; and impair the transmission of light into the leaf and lower canopy where photosynthesis is light limited. Consequently, decreasing leaf chlorophyll content of upper canopy leaves is considered an effective means to improving photosynthetic resource-use efficiency.

“Non-photochemical quenching” is a term that covers photoprotective processes that dissipate absorbed light energy as heat from the light-harvesting antenna of photosystem II. Non-photochemical quenching is a key regulator of the efficiency with which electron transport is initiated by PSII and the efficiency of photosynthesis at low light. Decreasing the level of non-photochemical quenching, or increasing the speed with which it relaxes is expected to confer cumulative gains in photosynthesis every time the light intensity to which the canopy is exposed transitions from high to low, and is considered a means to improving canopy photosynthesis when integrated over a growing season.

“Nitrogen limitation” or “nitrogen-limiting” refers to nitrogen levels that act as net limitations on primary production in terrestrial or aquatic biomes. Much of terrestrial growth, including much of crop growth, is limited by the availability of nitrogen, which can be alleviated by nitrogen input through deposition or fertilization.

“Water use efficiency”, or WUE, measured as the biomass produced per unit transpiration, describes the relationship between water use and crop production. The basic physiological definition of WUE equates to the ratio of photosynthesis (A) to transpiration (T), also referred to as transpiration efficiency (Karaba et al. 2007, supra; Morison et al., 2008, supra).

“Stomatal conductance” refers to a measurement of the limitation that the stomatal pore imposes on CO₂ diffusion into, and H₂O diffusion out of, the leaf. Decreasing stomatal conductance will decrease water loss from the leaf and crop canopy via transpiration. This will conserve soil water, delay the onset and reduce the severity of drought effects on canopy photosynthesis and other physiology. Decreasing stomatal conductance will also decrease photosynthesis. However, the magnitude of the decrease in photosynthesis will typically be less than the decrease in transpiration, and transpiration efficiency will increase as a result. Conversely, increasing stomatal conductance can increase the diffusion of CO₂ into the leaf and increase photosynthesis in a C3 leaf. Typically, transpiration will increase to a greater extent than photosynthesis, and transpiration efficiency will therefore decrease.

“Yield” or “plant yield” refers to increased plant growth, increased crop growth, increased biomass, and/or increased plant product production (including grain), and is dependent to some extent on temperature, plant size, organ size, planting density, light, water and nutrient availability, and how the plant copes with various stresses, such as through temperature acclimation and water or nutrient use efficiency. For grain crops, yield generally refers to an amount of grain produced or harvested per unit of land area, such as bushels or tons per acre or tonnes per hectare. Increased or improved yield may be measured as increased seed yield, increased plant product yield (plant products include, for example, plant tissue, including ground or otherwise broken-up plant tissue, and products derived from one or more types of plant tissue), or increased vegetative yield.

DESCRIPTION OF THE SPECIFIC EMBODIMENTS

Regulatory Polypeptides Modify Expression of Endogenous Genes.

A regulatory polypeptide may include, but is not limited to, any polypeptide that can activate or repress transcription of a single gene or a number of genes. As one of ordinary skill in the art recognizes, regulatory polypeptides can be identified by the presence of a region or domain of structural similarity or identity to a specific consensus sequence or the presence of a specific consensus DNA-binding motif (see, for example, Riechmann et al., 2000a. supra).

Generally, regulatory polypeptides control the manner in which information encoded by genes is used to produce gene products and control various pathways, and may be involved in diverse processes including, but not limited to, cell differentiation, proliferation, morphogenesis, and the regulation of growth or environmental responses. Accordingly, one skilled in the art would recognize that by expressing the present sequences in a plant, one may change the expression of autologous genes or induce the expression of introduced genes. By affecting the expression of similar autologous sequences in a plant that have the biological activity of the present sequences, or by introducing the present sequences into a plant, one may alter a plant's phenotype to one with improved traits related to photosynthetic resource use efficiency. The sequences of the instant description may also be used to transform a plant and introduce desirable traits not found in the wild-type cultivar or strain. Plants may then be selected for those that produce the most desirable degree of over- or under-expression of target genes of interest and coincident trait improvement.

The sequences of the present description may be from any species, particularly plant species, in a naturally occurring form or from any source whether natural, synthetic, semi-synthetic or recombinant. The sequences of the instant description may also include fragments of the present amino acid sequences. Where “amino acid sequence” is recited to refer to an amino acid sequence of a naturally occurring protein molecule, “amino acid sequence” and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule.

In addition to methods for modifying a plant phenotype by employing one or more polynucleotides and polypeptides of the instant description described herein, the polynucleotides and polypeptides of the instant description have a variety of additional uses. These uses include their use in the recombinant production (i.e., expression) of proteins; as regulators of plant gene expression, as diagnostic probes for the presence of complementary or partially complementary nucleic acids (including for detection of natural coding nucleic acids); as substrates for further reactions, e.g., mutation reactions, PCR reactions, or the like; as substrates for cloning e.g., including digestion or ligation reactions; and for identifying exogenous or endogenous modulators of the regulatory polypeptides. The polynucleotide can be, e.g., genomic DNA or RNA, a transcript (such as an mRNA), a cDNA, a PCR product, a cloned DNA, a synthetic DNA or RNA, or the like. The polynucleotide can comprise a sequence in either sense or antisense orientations.

Expression of genes that encode polypeptides that modify expression of endogenous genes, polynucleotides, and proteins are well known in the art. In addition, transgenic plants comprising polynucleotides encoding regulatory polypeptides may also modify expression of endogenous genes, polynucleotides, and proteins. Examples include Peng et al., 1997. Genes Development 11: 3194-3205, and Peng et al., 1999. Nature 400: 256-261. In addition, many others have demonstrated that an Arabidopsis regulatory polypeptide expressed in an exogenous plant species elicits the same or very similar phenotypic response. See, for example, Fu et al., 2001. Plant Cell 13: 1791-1802; Nandi et al., 2000. Curr. Biol. 10: 215-218; Coupland, 1995. Nature 377: 482-483; and Weigel and Nilsson, 1995. Nature 377: 482-500.

In another example, Mandel et al., 1992b. Cell 71-133-143, and Suzuki et al., 2001. Plant J. 28: 409-418, teach that a transcription factor expressed in another plant species elicits the same or very similar phenotypic response of the endogenous sequence, as often predicted in earlier studies of Arabidopsis transcription factors in Arabidopsis (see Mandel et al., 1992a. Nature 360: 273-277; Suzuki et al., 2001. supra). Other examples include Müller et al., 2001. Plant J. 28: 169-179; Kim et al., 2001. Plant J. 25: 247-259; Kyozuka and Shimamoto, 2002. Plant Cell Physiol. 43: 130-135; Boss and Thomas, 2002. Nature, 416: 847-850; He et al., 2000. Transgenic Res. 9: 223-227; and Robson et al., 2001. Plant J. 28: 619-631.

In yet another example, Gilmour et al., 1998. Plant J. 16: 433-442 teach an Arabidopsis AP2 transcription factor, CBF1, which, when overexpressed in transgenic plants, increases plant freezing tolerance. Jaglo et al., 2001. Plant Physiol. 127: 910-917, further identified sequences in Brassica napus which encode CBF-like genes and that transcripts for these genes accumulated rapidly in response to low temperature. Transcripts encoding CBF proteins were also found to accumulate rapidly in response to low temperature in wheat, as well as in tomato. An alignment of the CBF proteins from Arabidopsis, B. napus, wheat, rye, and tomato revealed the presence of conserved consecutive amino acid residues which bracket the AP2/EREBP DNA binding domains of the proteins and distinguish them from other members of the AP2/EREBP protein family (Jaglo et al., 2001. supra).

Regulatory polypeptides mediate cellular responses and control traits through altered expression of genes containing cis-acting nucleotide sequences that are targets of the introduced regulatory polypeptide. It is well appreciated in the art that the effect of a regulatory polypeptide on cellular responses or a cellular trait is determined by the particular genes whose expression is either directly or indirectly (e.g., by a cascade of regulatory polypeptide binding events and transcriptional changes) altered by regulatory polypeptide binding. In a global analysis of transcription comparing a standard condition with one in which a regulatory polypeptide is overexpressed, the resulting transcript profile associated with regulatory polypeptide overexpression is related to the trait or cellular process controlled by that regulatory polypeptide. For example, the PAP2 gene and other genes in the Myb family have been shown to control anthocyanin biosynthesis through regulation of the expression of genes known to be involved in the anthocyanin biosynthetic pathway (Bruce et al., 2000. Plant Cell 12: 65-79; and Borevitz et al., 2000. Plant Cell 12: 2383-2393). Further, global transcript profiles have been used successfully as diagnostic tools for specific cellular states (e.g., cancerous vs. non-cancerous; Bhattacharjee et al., 2001. Proc. Natl. Acad. Sci. USA 98: 13790-13795; and Xu et al., 2001. Proc. Natl. Acad. Sci. USA 98: 15089-15094). Consequently, it is evident to one skilled in the art that similarity of transcript profile upon overexpression of different regulatory polypeptides would indicate similarity of regulatory polypeptide function.

Polypeptides and Polynucleotides of the Present Description.

The present description includes putative regulatory polypeptides, and isolated or recombinant polynucleotides encoding the polypeptides, or novel sequence variant polypeptides or polynucleotides encoding novel variants of polypeptides derived from the specific sequences provided in the Sequence Listing; the recombinant polynucleotides of the instant description may be incorporated in expression vectors for the purpose of producing transformed plants.

Because of their relatedness at the nucleotide level, the claimed sequences will typically share at least about 30% nucleotide sequence identity, or at least 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% sequence identity to one or more of the listed full-length sequences, or to a listed sequence but excluding or outside of the region(s) encoding a known consensus sequence or consensus DNA-binding site, or outside of the region(s) encoding one or all conserved domains. The degeneracy of the genetic code enables major variations in the nucleotide sequence of a polynucleotide while maintaining the amino acid sequence of the encoded protein.

Because of their relatedness at the protein level, the claimed nucleotide sequences will typically encode a polypeptide that is at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical in its amino acid sequence to the entire length of any of the polypeptides listed in the Sequence Listing or the instant Tables, or closely- or phylogenetically-related sequences.

Also provided are methods for modifying yield from a plant by modifying the mass, size or number of plant organs or seed of a plant by controlling a number of cellular processes, and for increasing a plant's photosynthetic resource use efficiency. These methods are based on the ability to alter the expression of critical regulatory molecules that may be conserved between diverse plant species. Related conserved regulatory molecules may be originally discovered in a model system such as Arabidopsis and homologous, functional molecules then discovered in other plant species. The latter may then be used to confer increased yield or photosynthetic resource use efficiency in diverse plant species.

Sequences in the Sequence Listing, derived from diverse plant species, may be ectopically expressed in overexpressor plants. The changes in the characteristic(s) or trait(s) of the plants may then be observed and found to confer increased yield and/or increased photosynthetic resource use efficiency. Therefore, the polynucleotides and polypeptides can be used to improve desirable characteristics of plants.

The polynucleotides of the instant description are also ectopically expressed in overexpressor plant cells and the changes in the expression levels of a number of genes, polynucleotides, and/or proteins of the plant cells observed. Therefore, the polynucleotides and polypeptides can be used to change expression levels of genes, polynucleotides, and/or proteins of plants or plant cells.

The data presented herein represent the results obtained in experiments with polynucleotides and polypeptides that may be expressed in plants for the purpose of increasing yield that arises from improved photosynthetic resource use efficiency.

Variants of the Disclosed Sequences.

Also within the scope of the instant description is a variant of a nucleic acid listed in the Sequence Listing, that is, one having a sequence that differs from the one of the polynucleotide sequences in the Sequence Listing, or a complementary sequence, that encodes a functionally equivalent polypeptide (i.e., a polypeptide having some degree of equivalent or similar biological activity) but differs in sequence from the sequence in the Sequence Listing, due to degeneracy in the genetic code. Included within this definition are polymorphisms that may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding polypeptide, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding polypeptide.

Differences between presently disclosed polypeptides and polypeptide variants are limited so that the sequences of the former and the latter are closely similar overall and, in many regions, identical. Presently disclosed polypeptide sequences and similar polypeptide variants may differ in amino acid sequence by one or more substitutions, additions, deletions, fusions and truncations, which may be present in any combination. These differences may produce silent changes and result in a functionally equivalent polypeptides. Thus, it will be readily appreciated by those of skill in the art, that any of a variety of polynucleotide sequences is capable of encoding the polypeptides and homolog polypeptides of the instant description. A polypeptide sequence variant may have “conservative” changes, wherein a substituted amino acid has similar structural or chemical properties.

Conservative substitutions include substitutions in which at least one residue in the amino acid sequence has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the Table 1 when it is desired to maintain the activity of the protein. Table 1 shows amino acids which can be substituted for an amino acid in a protein and which are typically regarded as conservative substitutions.

TABLE 1 Possible conservative amino acid substitutions Amino Acid Conservative Amino Acid Conservative Residue substitutions Residue substitutions Ala Ser Leu Ile; Val Arg Lys Lys Arg; Gln Asn Gln; His Met Leu; Ile Asp Glu Phe Met; Leu; Tyr Gln Asn Pro Gly Cys Ser Ser Thr; Gly Glu Asp Thr Ser; Val Gly Pro Trp Tyr His Asn; Gln Tyr Trp; Phe He Leu, Val Val Ile; Leu

The polypeptides provided in the Sequence Listing have a novel activity, such as, for example, regulatory activity. Although all conservative amino acid substitutions (for example, one basic amino acid substituted for another basic amino acid) in a polypeptide will not necessarily result in the polypeptide retaining its activity, it is expected that many of these conservative mutations would result in the polypeptide retaining its activity. Most mutations, conservative or non-conservative, made to a protein but outside of a conserved domain required for function and protein activity will not affect the activity of the protein to any great extent.

Deliberate amino acid substitutions may thus be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as a significant amount of the functional or biological activity of the polypeptide is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, positively charged amino acids may include lysine and arginine, and amino acids with uncharged polar head groups having similar hydrophilicity values may include leucine, isoleucine, and valine; glycine and alanine; asparagine and glutamine; serine and threonine; and phenylalanine and tyrosine. More rarely, a variant may have “non-conservative” changes, e.g., replacement of a glycine with a tryptophan Similar minor variations may also include amino acid deletions or insertions, or both. Related polypeptides may comprise, for example, additions and/or deletions of one or more N-linked or O-linked glycosylation sites, or an addition and/or a deletion of one or more cysteine residues. Guidance in determining which and how many amino acid residues may be substituted, inserted or deleted without abolishing functional or biological activity may be found using computer programs well known in the art, for example, DNASTAR software (see U.S. Pat. No. 5,840,544).

Conserved Domains.

Conserved domains are recurring functional and/or structural units of a protein sequence within a protein family (for example, a family of regulatory proteins), and distinct conserved domains have been used as building blocks in molecular evolution and recombined in various arrangements to make proteins of different protein families with different functions. Conserved domains often correspond to the 3-dimensional domains of proteins and contain conserved sequence patterns or motifs, which allow for their detection in polypeptide sequences with, for example, the use of a Conserved Domain Database (for example, at www.ncbi.nlm.nih.gov/cdd). The National Center for Biotechnology Information Conserved Domain Database defines conserved domains as recurring units in molecular evolution, the extents of which can be determined by sequence and structure analysis. Conserved domains contain conserved sequence patterns or motifs, which allow for their detection in polypeptide sequences (Conserved Domain Database; www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml).

Conserved domains may also be identified as regions or domains of identity to a specific consensus sequence (see, for example, Riechmann et al., 2000a. Science 290, 2105-2110; Riechmann et al., 2000b. Curr Opin Plant Biol 3: 423-434). Thus, by using alignment methods well known in the art, the conserved domains of the plant polypeptides, for example, for the Myb domain polypeptides may be determined. The polypeptides of the instant Tables have conserved domains associated with the disclosed functions of the proteins in which they are found and specifically indicated by amino acid coordinate start and stop sites. A comparison of the regions of these polypeptides allows one of skill in the art (see, for example, Reeves and Nissen, 1990. J. Biol. Chem. 265, 8573-8582; Reeves and Nissen, 1995. Prog. Cell Cycle Res. 1: 339-349) to identify domains or conserved domains for any of the polypeptides listed or referred to in this disclosure.

Conserved domain models are generally identified with multiple sequence alignments of related proteins spanning a variety of organisms (for example, conserved domains of the disclosed sequences can be found in the instant Figures, Tables, and the Sequence Listing). These alignments reveal sequence regions containing the same, or similar, patterns of amino acids. Multiple sequence alignments, three-dimensional structure and three-dimensional structure superposition of conserved domains can be used to infer sequence, structure, and functional relationships (Conserved Domain Database, supra). Since the presence of a particular conserved domain within a polypeptide (prophetically including any of the instantly listed polypeptides) is highly correlated with an evolutionarily conserved function, a conserved domain database may be used to identify the amino acids in a protein sequence that are putatively involved in functions such as binding or catalysis, as mapped from conserved domain annotations to the query sequence. For example, the presence in a protein of Myb domain that is structurally and phylogenetically similar to one or more domains shown in the instant Tables would be a strong indicator of a related function in plants (e.g., the function of regulating and/or improving yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant; i.e., a polypeptide with such a domain is expected to confer altered yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant when its expression level is altered). Sequences herein referred to as functionally-related and/or closely-related to the sequences or domains listed in the instant Tables, including polypeptides that are closely related to the polypeptides of the instant description, may have conserved domains that share at least at least nine base pairs (bp) in length and at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to the sequences provided in the Sequence Listing or in the instant Tables, and have similar functions in that the polypeptides of the instant description. Said polypeptides may, when their expression level is altered by suppressing their expression, knocking out their expression, or increasing their expression, confer at least one regulatory activity selected from the group consisting of increased yield, increased light use efficiency, increased photosynthetic capacity, increased photosynthetic rate, increased photosynthetic resource use efficiency, greater vigor, and/or greater biomass as compared to a control plant.

Methods using manual alignment of sequences similar or homologous to one or more polynucleotide sequences or one or more polypeptides encoded by the polynucleotide sequences may be used to identify regions of similarity and conserved domains or other motifs. Such manual methods are well-known of those of skill in the art and can include, for example, comparisons of tertiary structure between a polypeptide sequence encoded by a polynucleotide that comprises a known function and a polypeptide sequence encoded by a polynucleotide sequence that has a function not yet determined. Such examples of tertiary structure may comprise predicted alpha helices, beta-sheets, amphipathic helices, leucine zipper motifs, zinc finger motifs, proline-rich regions, cysteine repeat motifs, and the like.

With respect to polynucleotides encoding presently disclosed polypeptides, a conserved domain refers to a subsequence within a polypeptide family (for example, in any of the instantly listed polypeptides or members of the listed polypeptide families) the presence of which is correlated with at least one function exhibited by members of the polypeptide family, and which exhibits a high degree of sequence homology, such as at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identity to a conserved domain of a polypeptide of the Sequence Listing or listed in the instant Tables that show the instant polypeptides and closely-related or phylogenetically-related sequences. Sequences that possess or encode for conserved domains that meet these criteria of percentage identity, and that have comparable biological and regulatory activity to the present polypeptide sequences, thus being members of the clade polypeptides or sequences listed in the sequence Listing or in Example I, are described. Sequences having lesser degrees of identity but comparable biological activity are considered to be equivalents.

Orthologs and Paralogs.

Homologous sequences as described above can comprise orthologous or paralogous sequences. Several different methods are known by those of skill in the art for identifying and defining these functionally homologous sequences. General methods for identifying orthologs and paralogs, including phylogenetic methods, sequence similarity and hybridization methods, are described herein; an ortholog or paralog, including equivalogs, may be identified by one or more of the methods described below.

As described by Eisen, 1998. Genome Res. 8: 163-167, evolutionary information may be used to predict gene function. It is common for groups of genes that are homologous in sequence to have diverse, although usually related, functions. However, in many cases, the identification of homologs is not sufficient to make specific predictions because not all homologs have the same function. Thus, an initial analysis of functional relatedness based on sequence similarity alone may not provide one with a means to determine where similarity ends and functional relatedness begins. Fortunately, it is well known in the art that protein function can be classified using phylogenetic analysis of gene trees combined with the corresponding species. Functional predictions can be greatly improved by focusing on how the genes became similar in sequence (i.e., by evolutionary processes) rather than on the sequence similarity itself (Eisen, supra). In fact, many specific examples exist in which gene function has been shown to correlate well with gene phylogeny (Eisen, supra). Thus, “[t]he first step in making functional predictions is the generation of a phylogenetic tree representing the evolutionary history of the gene of interest and its homologs. Such trees are distinct from clusters and other means of characterizing sequence similarity because they are inferred by techniques that help convert patterns of similarity into evolutionary relationships . . . . After the gene tree is inferred, biologically determined functions of the various homologs are overlaid onto the tree. Finally, the structure of the tree and the relative phylogenetic positions of genes of different functions are used to trace the history of functional changes, which is then used to predict functions of [as yet] uncharacterized genes” (Eisen, supra).

Within a single plant species, gene duplication may cause two copies of a particular gene, giving rise to two or more genes with similar sequence and often similar function known as paralogs. A paralog is therefore a similar gene formed by duplication within the same species. Paralogs typically cluster together or in the same clade (a group of similar genes) when a gene family phylogeny is analyzed using programs such as CLUSTAL (Thompson et al., 1994. Nucleic Acids Res. 22: 4673-4680; Higgins et al., 1996. Methods Enzymol. 266: 383-402). Groups of similar genes can also be identified with pair-wise BLAST analysis (Feng and Doolittle, 1987. J. Mol. Evol. 25: 351-360). For example, a clade of very similar MADS domain transcription factors from Arabidopsis all share a common function in flowering time (Ratcliffe et al., 2001. Plant Physiol. 126: 122-132), and a group of very similar AP2 domain transcription factors from Arabidopsis are involved in tolerance of plants to freezing (Gilmour et al., 1998. supra). Analysis of groups of similar genes with similar function that fall within one clade can yield sub-sequences that are particular to the clade. These sub-sequences, known as consensus sequences, can not only be used to define the sequences within each clade, but define the functions of these genes; genes within a clade may contain paralogous sequences, or orthologous sequences that share the same function (see also, for example, Mount, 2001, in Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., p. 543).

Regulatory polypeptide gene sequences are conserved across diverse eukaryotic species lines (Goodrich et al., 1993. Cell 75:519-530; Lin et al., 1991. Nature 353:569-571; Sadowski et al., 1988. Nature 335: 563-564). Plants are no exception to this observation; diverse plant species possess regulatory polypeptides that have similar sequences and functions. Speciation, the production of new species from a parental species, gives rise to two or more genes with similar sequence and similar function. These genes, termed orthologs, often have an identical function within their host plants and are often interchangeable between species without losing function. Because plants have common ancestors, many genes in any plant species will have a corresponding orthologous gene in another plant species. Once a phylogenic tree for a gene family of one species has been constructed using a program such as CLUSTAL (Thompson et al., 1994. supra; Higgins et al., 1996. supra) potential orthologous sequences can be placed into the phylogenetic tree and their relationship to genes from the species of interest can be determined. Orthologous sequences can also be identified by a reciprocal BLAST strategy. Once an orthologous sequence has been identified, the function of the ortholog can be deduced from the identified function of the reference sequence.

By using a phylogenetic analysis, one skilled in the art would recognize that the ability to deduce similar functions conferred by closely-related polypeptides is predictable. This predictability has been confirmed by our own many studies in which we have found that a wide variety of polypeptides have orthologous or closely-related homologous sequences that function as does the first, closely-related reference sequence. For example, distinct regulatory polypeptides, including:

(i) AP2 family Arabidopsis G47 (found in U.S. Pat. No. 7,135,616), a phylogenetically-related sequence from soybean, and two phylogenetically-related homologs from rice all can confer greater tolerance to drought, hyperosmotic stress, or delayed flowering as compared to control plants;

(ii) CAAT family Arabidopsis G481 (found in PCT patent publication no. WO2004076638), and numerous phylogenetically-related sequences from eudicots and monocots can confer greater tolerance to drought-related stress as compared to control plants;

(iii) Myb-related Arabidopsis G682 (found in U.S. Pat. Nos. 7,223,904 and 7,193,129) and numerous phylogenetically-related sequences from eudicots and monocots can confer greater tolerance to heat, drought-related stress, cold, and salt as compared to control plants;

(iv) WRKY family Arabidopsis G1274 (found in U.S. Pat. No. 7,196,245) and numerous closely-related sequences from eudicots and monocots have been shown to confer increased water deprivation tolerance, and

(v) AT-hook family soy sequence G3456 (found in U.S. patent publication no. 20040128712A1) and numerous phylogenetically-related sequences from eudicots and monocots, increased biomass compared to control plants when these sequences are overexpressed in plants.

Examples of Methods for Identifying Identity, Similarity, Homology and Relatedness.

Percent identity can be determined electronically, e.g., by using the MEGALIGN program (DNASTAR, Inc. Madison, Wis.). The MEGALIGN program can create alignments between two or more sequences according to different methods, for example, the clustal method (see, for example, Higgins and Sharp, 1988. Gene 73: 237-244). The clustal algorithm groups sequences into clusters by examining the distances between all pairs. The clusters are aligned pairwise and then in groups. Other alignment algorithms or programs may be used for preparing alignments and/or determining percentage identities, including Accelrys Gene, FASTA, BLAST, or ENTREZ, FASTA and BLAST, some of which may also be used to calculate percent similarity. Accelrys Gene is available from Accelrys, Inc., San Diego, Calif. Other programs are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with or without default settings. ENTREZ is available through the National Center for Biotechnology Information. In one embodiment, the percent identity of two sequences can be determined by the GCG program with a gap weight of 1, e.g., each amino acid gap is weighted as if it were a single amino acid or nucleotide mismatch between the two sequences (see U.S. Pat. No. 6,262,333).

Software for performing BLAST analyses is publicly available, e.g., through the National Center for Biotechnology Information (see internet website at www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul, 1990. J. Mol. Biol. 215: 403-410; Altschul, 1993. J. Mol. Evol. 36: 290-300). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff, 1989. supra; Henikoff and Henikoff, 1991. supra). Unless otherwise indicated for comparisons of predicted polynucleotides, “sequence identity” refers to the % sequence identity generated from a tBLASTx using the NCBI version of the algorithm at the default settings using gapped alignments with the filter “off” (see, for example, internet website at www.ncbi.nlm.nih.gov).

Other techniques for alignment are described by Doolittle, ed., 1996. Methods in Enzymology, vol. 266: “Computer Methods for Macromolecular Sequence Analysis” Academic Press, Inc., San Diego, Calif., USA. Preferably, an alignment program that permits gaps in the sequence is utilized to align the sequences. The Smith-Waterman is one type of algorithm that permits gaps in sequence alignments (see Shpaer, 1997. Methods Mol. Biol. 70: 173-187). Also, the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. An alternative search strategy uses MPSRCH software, which runs on a MASPAR computer. MPSRCH uses a Smith-Waterman algorithm to score sequences on a massively parallel computer. This approach improves ability to pick up distantly related matches, and is especially tolerant of small gaps and nucleotide sequence errors. Nucleic acid-encoded amino acid sequences can be used to search both protein and DNA databases.

The percentage similarity between two polypeptide sequences, e.g., sequence A and sequence B, is calculated by dividing the length of sequence A, minus the number of gap residues in sequence A, minus the number of gap residues in sequence B, into the sum of the residue matches between sequence A and sequence B, times one hundred. Gaps of low or of no similarity between the two amino acid sequences are not included in determining percentage similarity. Percent identity between polynucleotide sequences can also be counted or calculated by other methods known in the art, e.g., the Jotun Hein method (see, for example, Hein, 1990. Methods Enzymol. 183: 626-645). Identity between sequences can also be determined by other methods known in the art, e.g., by varying hybridization conditions (see U.S. patent publication no. 20010010913).

The percent identity between two polypeptide sequences can also be determined using Accelrys Gene v2.5, 2006 with default parameters: Pairwise Matrix: GONNET; Align Speed: Slow; Open Gap Penalty: 10.000; Extended Gap Penalty: 0.100; Multiple Matrix: GONNET; Multiple Open Gap Penalty: 10.000; Multiple Extended Gap Penalty: 0.05; Delay Divergent: 30; Gap Separation Distance: 8; End Gap Separation: false; Residue Specific Penalties: false; Hydrophilic Penalties: false; Hydrophilic Residues: GPSNDQEKR. The default parameters for determining percent identity between two polynucleotide sequences using Accelrys Gene are: Align Speed: Slow; Open Gap Penalty: 10.000; Extended Gap Penalty: 5.000; Multiple Open Gap Penalty: 10.000; Multiple Extended Gap Penalty: 5.000; Delay Divergent: 40; Transition: Weighted.

In addition, one or more polynucleotide sequences or one or more polypeptides encoded by the polynucleotide sequences may be used to search against a BLOCKS (Bairoch et al., 1997. Nucleic Acids Res. 25: 217-221), PFAM, and other databases which contain previously identified and annotated motifs, sequences and gene functions. Methods that search for primary sequence patterns with secondary structure gap penalties (Smith et al., 1992. Protein Engineering 5: 35-51) as well as algorithms such as Basic Local Alignment Search Tool (BLAST; Altschul, 1990, supra; Altschul et al., 1993, supra), BLOCKS (Henikoff and Henikoff, 1991, supra), Hidden Markov Models (HMM; Eddy, 1996. Curr. Opin. Str. Biol. 6: 361-365; Sonnhammer et al., 1997. Proteins 28: 405-420), and the like, can be used to manipulate and analyze polynucleotide and polypeptide sequences encoded by polynucleotides. These databases, algorithms and other methods are well known in the art and are described in Ausubel et al., 1997. Short Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y., unit 7.7, and in Meyers, 1995. Molecular Biology and Biotechnology, Wiley VCH, New York, N.Y., p 856-853.

Thus, the instant description provides methods for identifying a sequence similar or paralogous or orthologous or homologous to one or more polynucleotides as noted herein, or one or more target polypeptides encoded by the polynucleotides, or otherwise noted herein and may include linking or associating a given plant phenotype or gene function with a sequence. In the methods, a sequence database is provided (locally or across an internet or intranet) and a query is made against the sequence database using the relevant sequences herein and associated plant phenotypes or gene functions.

A further method for identifying or confirming that specific homologous sequences control the same function is by comparison of the transcript profile(s) obtained upon overexpression or knockout of two or more related polypeptides. Since transcript profiles are diagnostic for specific cellular states, one skilled in the art will appreciate that genes that have a highly similar transcript profile (e.g., with greater than 50% regulated transcripts in common, or with greater than 70% regulated transcripts in common, or with greater than 90% regulated transcripts in common) will have highly similar functions. Fowler and Thomashow, 2002. Plant Cell 14, 1675-1690, have shown that three paralogous AP2 family genes (CBF1, CBF2 and CBF3) are induced upon cold treatment, each of which can condition improved freezing tolerance, and all have highly similar transcript profiles. Once a polypeptide has been shown to provide a specific function, its transcript profile becomes a diagnostic tool to determine whether paralogs or orthologs have the same function.

Identifying Polynucleotides or Nucleic Acids by Hybridization.

Polynucleotides homologous to the sequences illustrated in the Sequence Listing and tables can be identified, e.g., by hybridization to each other under stringent or under highly stringent conditions. Stringency is influenced by a variety of factors, including temperature, salt concentration and composition, organic and non-organic additives, solvents, etc. present in both the hybridization and wash solutions and incubations, and the number of washes, as described in more detail in the references cited below (e.g., Sambrook et al., 1989. supra; Berger and Kimmel, eds., 1987. Methods Enzymol. 152: 507-511; Anderson and Young, 1985. “Quantitative Filter Hybridisation”, In: Hames and Higgins, ed., Nucleic Acid Hybridisation, A Practical Approach. Oxford, IRL Press, 73-111), each of which are incorporated herein by reference. Conditions that are highly stringent, and means for achieving them, are also well known in the art and described in, for example, Sambrook et al., 1989. supra; Berger and Kimmel, eds., 1987. Meth. Enzymol. 152:467-469; and Anderson and Young, 1985. supra.

Also provided in the instant description are polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, including any of the polynucleotides within the Sequence Listing, and fragments thereof under various conditions of stringency (see, for example, Wahl and Berger, 1987. Methods Enzymol. 152: 399-407; Berger and Kimmel, ed., 1987. Methods Enzymol. 152:507-511). In addition to the nucleotide sequences listed in the Sequence Listing, full length cDNA, orthologs, and paralogs of the present nucleotide sequences may be identified and isolated using well-known methods. The cDNA libraries, orthologs, and paralogs of the present nucleotide sequences may be screened using hybridization methods to determine their utility as hybridization target or amplification probes.

Stability of DNA duplexes is affected by such factors as base composition, length, and degree of base pair mismatch. Hybridization conditions may be adjusted to allow DNAs of different sequence relatedness to hybridize. The melting temperature (T_(m)) is defined as the temperature when 50% of the duplex molecules have dissociated into their constituent single strands. The melting temperature of a perfectly matched duplex, where the hybridization buffer contains formamide as a denaturing agent, may be estimated by the following equations: T _(m)(° C.)=81.5+16.6(log [Na+])+0.41(% G+C)−0.62(% formamide)−500/L  (I) DNA-DNA T _(m)(° C.)=79.8+18.5(log [Na+])+0.58(% G+C)+0.12(% G+C)²−0.5(% formamide)−820/L  (II) DNA-RNA T _(m)(° C.)=79.8+18.5(log [Na+])+0.58(% G+C)+0.12(% G+C)²−0.35(% formamide)−820/L  (III) RNA-RNA

where L is the length of the duplex formed, [Na+] is the molar concentration of the sodium ion in the hybridization or washing solution, and % G+C is the percentage of (guanine+cytosine) bases in the hybrid. For imperfectly matched hybrids, approximately 1° C. is required to reduce the melting temperature for each 1% mismatch.

Hybridization experiments are generally conducted in a buffer of pH between 6.8 to 7.4, although the rate of hybridization is nearly independent of pH at ionic strengths likely to be used in the hybridization buffer (Anderson and Young, 1985. supra). In addition, one or more of the following may be used to reduce non-specific hybridization: sonicated salmon sperm DNA or another non-complementary DNA, bovine serum albumin, sodium pyrophosphate, sodium dodecylsulfate (SDS), polyvinyl-pyrrolidone, ficoll and Denhardt's solution. Dextran sulfate and polyethylene glycol 6000 act to exclude DNA from solution, thus raising the effective probe DNA concentration and the hybridization signal within a given unit of time. In some instances, conditions of even greater stringency may be desirable or required to reduce non-specific and/or background hybridization. These conditions may be created with the use of higher temperature, lower ionic strength and higher concentration of a denaturing agent such as formamide.

Stringency conditions can be adjusted to screen for moderately similar fragments such as homologous sequences from distantly related organisms, or to highly similar fragments such as genes that duplicate functional enzymes from closely related organisms. The stringency can be adjusted either during the hybridization step or in the post-hybridization washes. Salt concentration, formamide concentration, hybridization temperature and probe lengths are variables that can be used to alter stringency (as described by the formula above). As a general guideline, high stringency is typically performed at T_(m)−5° C. to T_(m)−20° C., moderate stringency at T_(m)−20° C. to T_(m)−35° C. and low stringency at T_(m)−35° C. to T_(m)−50° C. for duplex >150 base pairs. Hybridization may be performed at low to moderate stringency (25-50° C. below T_(m)), followed by post-hybridization washes at increasing stringencies. Maximum rates of hybridization in solution are determined empirically to occur at T_(m)−25° C. for DNA-DNA duplex and T_(m)−15° C. for RNA-DNA duplex. Optionally, the degree of dissociation may be assessed after each wash step to determine the need for subsequent, higher stringency wash steps.

High stringency conditions may be used to select for nucleic acid sequences with high degrees of identity to the disclosed sequences. An example of stringent hybridization conditions obtained in a filter-based method such as a Southern or Northern blot for hybridization of complementary nucleic acids that have more than 100 complementary residues is about 5° C. to 20° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and pH. Conditions used for hybridization may include about 0.02 M to about 0.15 M sodium chloride, about 0.5% to about 5% casein, about 0.02% SDS or about 0.1% N-laurylsarcosine, about 0.001 M to about 0.03 M sodium citrate, at hybridization temperatures between about 50° C. and about 70° C. More preferably, high stringency conditions are about 0.02 M sodium chloride, about 0.5% casein, about 0.02% SDS, about 0.001 M sodium citrate, at a temperature of about 50° C. Nucleic acid molecules that hybridize under stringent conditions will typically hybridize to a probe based on either the entire DNA molecule or selected portions, e.g., to a unique subsequence, of the DNA.

Stringent salt concentration will ordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate. Increasingly stringent conditions may be obtained with less than about 500 mM NaCl and 50 mM trisodium citrate, to even greater stringency with less than about 250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, whereas high stringency hybridization may be obtained in the presence of at least about 35% formamide, and more preferably at least about 50% formamide. Stringent temperature conditions will ordinarily include temperatures of at least about 30° C., more preferably of at least about 37° C., and most preferably of at least about 42° C. with formamide present. Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS) and ionic strength, are well known to those skilled in the art. Various levels of stringency are accomplished by combining these various conditions as needed.

The washing steps that follow hybridization may also vary in stringency; the post-hybridization wash steps primarily determine hybridization specificity, with the most critical factors being temperature and the ionic strength of the final wash solution. Wash stringency can be increased by decreasing salt concentration or by increasing temperature. Stringent salt concentration for the wash steps will preferably be less than about 30 mM NaCl and 3 mM trisodium citrate, and most preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate.

Thus, high stringency hybridization and wash conditions that may be used to bind and remove polynucleotides with less than the desired homology to the nucleic acid sequences or their complements that encode the present polypeptides include, for example:

6×SSC at 65° C.;

50% formamide, 4×SSC at 42° C.; or

0.5×SSC, 0.1% SDS at 65° C.;

with, for example, two wash steps of 10-30 minutes each. Useful variations on these conditions will be readily apparent to those skilled in the art.

A person of skill in the art would not expect substantial variation among polynucleotide species provided with the present description because the highly stringent conditions set forth in the above formulae yield structurally similar polynucleotides.

If desired, one may employ wash steps of even greater stringency, including about 0.2×SSC, 0.1% SDS at 65° C. and washing twice, each wash step being about 30 minutes, or about 0.1×SSC, 0.1% SDS at 65° C. and washing twice for 30 minutes. The temperature for the wash solutions will ordinarily be at least about 25° C., and for greater stringency at least about 42° C. Hybridization stringency may be increased further by using the same conditions as in the hybridization steps, with the wash temperature raised about 3° C. to about 5° C., and stringency may be increased even further by using the same conditions except the wash temperature is raised about 6° C. to about 9° C. For identification of less closely related homologs, wash steps may be performed at a lower temperature, e.g., 50° C.

An example of a low stringency wash step employs a solution and conditions of at least 25° C. in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS over 30 minutes. Greater stringency may be obtained at 42° C. in 15 mM NaCl, with 1.5 mM trisodium citrate, and 0.1% SDS over 30 minutes. Even higher stringency wash conditions are obtained at 65° C.-68° C. in a solution of 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Wash procedures will generally employ at least two final wash steps. Additional variations on these conditions will be readily apparent to those skilled in the art (see, for example, U.S. patent publication no. 20010010913).

Stringency conditions can be selected such that an oligonucleotide that is perfectly complementary to the coding oligonucleotide hybridizes to the coding oligonucleotide with at least about a 5-10× higher signal to noise ratio than the ratio for hybridization of the perfectly complementary oligonucleotide to a nucleic acid encoding a polypeptide known as of the filing date of the application. It may be desirable to select conditions for a particular assay such that a higher signal to noise ratio, that is, about 15× or more, is obtained. Accordingly, a subject nucleic acid will hybridize to a unique coding oligonucleotide with at least a 2× or greater signal to noise ratio as compared to hybridization of the coding oligonucleotide to a nucleic acid encoding known polypeptide. The particular signal will depend on the label used in the relevant assay, e.g., a fluorescent label, a colorimetric label, a radioactive label, or the like. Labeled hybridization or PCR probes for detecting related polynucleotide sequences may be produced by oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide.

The present description also provides polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, including any of the polynucleotides within the Sequence Listing, and fragments thereof under various conditions of stringency (see, for example, Wahl and Berger, 1987, supra, pages 399-407; and Kimmel, 1987. Meth. Enzymol. 152, 507-511). In addition to the nucleotide sequences in the Sequence Listing, full length cDNA, orthologs, and paralogs of the present nucleotide sequences may be identified and isolated using well-known methods. The cDNA libraries, orthologs, and paralogs of the present nucleotide sequences may be screened using hybridization methods to determine their utility as hybridization target or amplification probes.

EXAMPLES

It is to be understood that this description is not limited to the particular devices, machines, materials and methods described. Although particular embodiments are described, equivalent embodiments may be used to practice the claims.

The specification, now being generally described, will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present description and are not intended to limit the claims or description. It will be recognized by one of skill in the art that a polypeptide that is associated with a particular first trait may also be associated with at least one other, unrelated and inherent second trait which was not predicted by the first trait.

Example I. The Instant Polynucleotides and their Encoded or Predicted Polypeptides

The instant polypeptides sequences belong to distinct clades of polypeptides that include members from diverse species. In each case, clade member sequences derived from both eudicots and monocots may be shown to confer increased yield or tolerance to one or more abiotic stresses when the sequences were overexpressed. These studies can demonstrate that evolutionarily conserved genes from diverse species are likely to function similarly (i.e., by regulating similar target sequences and controlling the same traits), and that polynucleotides from one species may be transformed into closely-related or distantly-related plant species to confer or improve traits.

The listed polypeptide sequences may be found within the polypeptide clades of Myb Domain Protein 27 (“AtMYB27”; AT3G53200; G1311), ACBF-like family member RNA-binding protein 45A (“RBP45A”; AT5G54900; G1940), PCF family member TEOSINTE BRANCHED1//CYCLOIDEA//PCF 6 transcription factor 6 (“TCP6”; AT5G41030; G1936), Basic helix-loop-helix protein (bHLH) family member Phytochrome Interacting Factor 3-like 1 (“PIL1”: AT2G46970; G1649), GARP family member PHYTOCLOCK 1 (“PCL1”; AT3G46640.3; G2741), TH family member GT-2-Likel (“GTL1”; AT1G33240; G634), AP2 family members Dehydration-Responsive Element-Binding Protein 2H (“DREB2H”; AT2G40350; G1755), and ethylene-responsive transcription factor ERF087 (“ERF087”; AT1G28160; G2292), CCAAT family member Nuclear Transcription Factor Y subunit C-6 (“NF-YC6”; AT5G50480; G1820), Z—CO-like family member CONSTANS-like B-box zinc finger protein (“BBX18”, “F3K23.8”; AT2G21320; G1881), HLH/MYC family member Basic Helix-Loop-Helix 60 (“bHLH60”; AT3G57800.2; G2144), Z—CO-like family member CONSTANS-like B-box zinc finger protein (“BBX26”, AT1G60250, G1486), bHLH family member bHLH121 (At3g19860, G782), and Putative MethylTransferase 24 (“PMT24” NP_174240, G837).

Orthologs and paralogs of presently disclosed polypeptides may be cloned using compositions provided by the present description according to methods well known in the art. cDNAs can be cloned using mRNA from a plant cell or tissue that expresses one of the present sequences. Appropriate mRNA sources may be identified by interrogating Northern blots with probes designed from the present sequences, after which a library is prepared from the mRNA obtained from a positive cell or tissue. Polypeptide-encoding cDNA is then isolated using, for example, PCR, using primers designed from a presently disclosed gene sequence, or by probing with a partial or complete cDNA or with one or more sets of degenerate probes based on the disclosed sequences. The cDNA library may be used to transform plant cells. Expression of the cDNAs of interest is detected using, for example, microarrays, Northern blots, quantitative PCR, or any other technique for monitoring changes in expression. Genomic clones may be isolated using similar techniques to those.

Examples of orthologs of the Arabidopsis polypeptide sequences and their functionally similar orthologs are listed in the instant Tables and the Sequence Listing. In addition to the sequences in the instant Tables and the Sequence Listing, the claimed nucleotide sequences are phylogenetically and structurally similar to sequences listed in the Sequence Listing and can function in a plant by increasing yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant when ectopically expressed, or overexpressed, in a plant. Since a significant number of these sequences are phylogenetically and sequentially related to each other and may be shown to increase yield from a plant and/or photosynthetic resource use efficiency, one skilled in the art would predict that other similar, phylogenetically related sequences falling within the present clades of polypeptides, including AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide sequences, would also perform similar functions when ectopically expressed.

Background Information for AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24, and their Clade Member Sequences.

A number of phylogenetically-related sequences have been found in other plant species. The instant Tables list a number of AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade sequences from diverse species. The tables include the SEQ ID NO: (Column 1), the species from which the sequence was derived and the Gene Identifier (“GID”; Column 2), the percent identity of the polypeptide in Column 1 to the first listed full length polypeptide (SEQ ID NO: 2, 42, 86, 108, 126, 156, 192, 246, 278, 318, 356, 388, 410, or 444), as determined by a BLASTp analysis, for example, with a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (Henikoff and Henikoff, 1989. Proc. Natl. Acad. Sci. USA 89:10915; Henikoff and Henikoff, 1991. Nucleic Acids Res. 19: 6565-6572) (Column 3), the amino acid residue coordinates for the conserved domains in amino acid coordinates beginning at the N-terminus, of each of the sequences (Column 4), the conserved domain sequences of the respective polypeptides (Column 5); the SEQ ID NO: of each of the domains (Column 6), and the percentage identity of the conserved domain in Column 5 to the conserved domain of the first listed sequence (as determined by a BLASTp analysis, wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix, and with the proportion of identical amino acids in parentheses; Column 7).

Species abbreviations that appear in Columns 2 of the following Tables include: At—Arabidopsis thaliana; Bd—Brachypodium distachyon; Cc—Citrus clementina; Eg—Eucalyptus grandis; Gm—Glycine max; Os—Oryza sativa; Pt—Populus trichocarpa; Si—Setaria italica; Sl—Solanum lycopersicum; Vv—Vitus vinifera; Zm—Zea mays.

AtMYB27 Clade Polypeptides

TABLE 2 Conserved ‘Myb domain 1’ of AtMYB27 and closely related sequences Col. 7 Percent identity Col. 3 Col. 4 of the Percent Myb Col. 6 Myb domain Col. 1 identity of domain 1 SEQ ID in Col. 5 to SEQ Col. 2 polypeptide in amino Col. 5 NO: of the Myb ID Species/ in Col. 1 to acid Conserved Myb Myb domain 1 of NO: Identifier AtMyb27 coordinates domain 1 domain 1 AtMyb27 2 At/AtMyb27 or 100% 11-58 RGPWLEEEDERLVKVI 483 100% (48/48) AT3G53200.1 (238/238) SLLGERRWDSLAIVSG LKRSGKSCRLRWMNY L 14 Vv/GSVIVT010  72%  8-55 KGSWLEEEDERLTAF 489  77% (37/48) 33670001  (83/115) VGLLGERRWDSIARA SGLKRSGKSCRLRWL NYL 4 Gm/G1yma10g0  44%  8-55 KGTWLQEEDEQLTSF 484  75% (36/48) 6680.1 (106/236) VTRLGERRWDSLAKV AGLKRSGKSCRLRWM NYL 6 Gm/Glyma13g2  70%  8-55 KGTWLQEEDEQLTSF 485  75% (36/48) 0880.1  (77/110) VARLGERRWDSLAKV AGLKRSGKSCRLRWM NYL 8 Cc/clementine0.  49% 38-85 KGPWHEEEDELLVTF 486  72% (35/48) 9_029544m  (90/182) VTLFGERRWDYIAKA SGLKRSGKSCRLRWL NYL 10 Eg/Eucgr.A016  43% 15-62 KGPWIEQEDEILTAFV 487  68% (33/48) 48.1 (102/234) TVLGERRWDYIAKTS GLKRSGKSCRLRWKN YL 12 Pt/POPTR_000  48% 10-57 KGSWQEEEDERLTAS 488  68% (33/48) 6s12400.1  (98/203) ATLLGERKWDSIARLS GLMRSGKSCRMRWL NYL

TABLE 3 Conserved ‘Myb domain 2’ of AtMYB27 and closely related sequences Col. 7 Percent identity Col. 3 Col. 4 of the Percent Myb Col. 6 Myb domain Col. 1 identity of domain 2 SEQ ID in Col. 5 to SEQ Col. 2 polypeptide in amino Col. 5 NO: of Myb ID Species/ in Col. 1 to acid Conserved Myb Myb domain 2 of NO: Identifier AtMyb27 coordinates domain 2 domain 2 AtMyb27 2 At/AtMyb27 or 100%  64-109 RGPMSQEEERIIFQLH 490 100% (46/46) AT3G53200.1 (238/238) ALWGNKWSKIARRL PGRTDNEIKNYWRTH Y 12 Pt/POPTR_000  48%  63-108 RGHISAEEEQIIIQFHG 495  77% (35/45) 6s12400.1  (98/203) QWGNKWARIARRLP GRTDNEIKNYWRTH M 14 Vv/GSVIVT01  72%  61-106 RCQISAEEEQIILQLH 496  76% (35/46) 033670001  (83/115) KRWGNKWSWIARSL PGRTDNEIKNYWRTH L 10 Eg/Eucgr.A016  43%  68-113 HGPISPEEERIIIKFHE 494  72% (32/44) 48.Eg/1 (102/234) QWGNKWSRIAEKLP GRTDNEIKNFWKTHL 4 Gm/Glyma10g0  44%  61-106 HGHFSVEEEQLIVQL 491  70% (31/44) 6680.1 (106/236) QQQLGNKWAKIARK LPGRTDNEIKNFVVRT HL 6 Gm/Glyma13g2  70%  61-106 HGHFSVEEEQLIVQL 492  68% (31/45) 0880.1  (77/110) QQELGNKWAKIARK LPGRTDNEIKNYWKT HL 8 Cc/clementine0.  49%  91-139 HGYISTEEEQIIIQLHK 493  63% (29/46) 9_029544m  (90/182) NIKIYLHGWSRIARSL PGRTDNEIKNCWRTR I

Sequences that are functionally-related and/or closely-related to the polypeptides in the above Tables may be created artificially, semi-synthetically, or may occur naturally by having descended from the same ancestral sequence as the disclosed closely-related sequences, where the polypeptides have the function of conferring increased photosynthetic resource use efficiency to plants.

These functionally-related and/or closely-related AtMYB27 clade polypeptides may be identified by a consensus first Myb domain (Myb domain 1) consensus sequence, SEQ ID NO: 842:

X¹GX³WX⁵X⁶X⁷EDEX¹¹LX¹³X¹⁴X¹⁵X¹⁶X¹⁷X¹⁸X¹⁹GERX²³WDX²⁶X²⁷AX²⁹X³⁰X³¹GLX³⁴RSGKSCR X⁴²RWX⁴⁵NYL

where X¹=K or R; X³=any amino acid; X⁵=any amino acid; X⁶=Q or E; X⁷=Q or E; X¹¹=any amino acid; X¹³=T or V; X¹⁴=any amino acid; X¹⁵=any amino acid; X¹⁶=any amino acid; X¹⁷=S, A, T or G; X¹⁸=any amino acid; X¹⁹=F, I, L, V or M; X²³=R or K; X²⁶=any amino acid; X²⁷=I, L, V or M; X²⁹=any amino acid; X³⁰=any amino acid; X³¹=S or A; X³⁴=any amino acid; X⁴²=I, L, V or M; and X⁴⁵=any amino acid.

These functionally-related and/or closely-related AtMYB27 clade polypeptides also may be identified by a consensus second Myb domain (Myb domain 2) consensus sequence, SEQ ID NO: 843:

X¹X²X³X⁴SX⁶EEEX¹⁰X¹¹IX¹³X¹⁴X¹⁵X¹⁶X¹⁷X¹⁸X¹⁹X²⁰X²¹X²²X²³X²⁴X²⁵WX²⁷X²⁸IAX³¹X³²LPGRTDN EIKNX⁴⁴WX⁴⁶TX⁴⁸X⁴⁹

where X¹=any amino acid; X²=any amino acid; X³=any amino acid; X⁴=F, I, L, V or M; X⁶=any amino acid; X¹⁰=any amino acid; X¹¹=I, L, V or M; X¹³=F, I, L, V or M; X¹⁴=Q or K; X¹⁵=F, I, L, V or M; X¹⁶=H or Q; X¹⁷=any amino acid; X¹⁸=any amino acid; X¹⁹=any amino acid; X²⁰=any amino acid; X²¹=any amino acid; X²²=any amino acid; X²³=L or absent; X²⁴=H or absent; X²⁵=G or absent; X²⁷=S or A; X²⁸=any amino acid; X³¹=any amino acid; X³²=any amino acid; X⁴⁴=any amino acid; X⁴⁶=K or R; X⁴⁸=any amino acid; and X⁴⁹=any amino acid. RBP45A Clade Polypeptides

TABLE 4 Conserved ‘RRM1 domain’ of RBP45A and closely related sequences Col. 7 Percent identity Col. 3 Col. 4 of RRM1 Percent RRM1 Col. 6 domain Col. 1 identity of domain SEQ ID in Col. 5 to SEQ Col. 2 polypeptide in amino Col. 5 NO: of RRM1 ID Species/ in Col. 1 to acid Conserved RRM1 RRM1 domain of NO: Identifier RBP45A coordinates domain domain RBP45A 42 At/RBP45A or 100%  61-141 SLWIGDLQQWMDE 510 100% AT5G54900.1 (387/387) NYIMSVFAQSGEAT (81/81) SAKVIRNKLTGQSE GYGFIEFVSHSVAER VLQTYNGAPMPSTE QTFRLNWAQAG 40 At/AT4G27000.1  71%  81-161 SLWIGDLQPWMDEN 509  79% (282/394) YLMNVFGLTGEATA (64/81) AKVIRNKQNGYSEG YGFIEFVNHATAER NLQTYNGAPMPSSE QAFRLNWAQLG 44 Pt/POPTR_000  70%  68-148 SLWIGDLQQWMDE 511  76% 1s45000.1 (228/323) NYILSIFSTTGEVVQ (62/81) AKVIRNKQTGYPEG YGFIEFVSHAAAERI LQTYNGTPMPNSEQ TFRLNWATLG 46 Pt/POPTR_001  69%  71-151 SLWIGDLQQWMDE 512  72% 1s14150.1 (231/331) NYLLSIFSATGEIVQ (59/81) AKVIRNKQTGYPEG YGFIEFVSRAAAERI LQTYNGTPMPNSEQ AFRLNWATLG 66 Sl/Solyc02g080  66%  80-160 SLWIGDLQFVVMDEQ 522  72% 420.2.1 (216/325) YLLNCFAQTGEVTS (59/81) AKVIRNKQSGQSEG YGFIEFISHAAAERN LQAYNGTLMPNIEQ NFRLNWASLG 68 Sl/Solyc10g005  65%  77-157 TLWIGDLQFWMDE 523  71% 260.2.1 (218/333) QYLYSCFAQTGEVV (58/81) SAKVIRNKQTQQSE GYGFIEFNSHAAAER NLQAYNGTLMPNIE QNFRLNWASLG 70 Sl/Solyc03g031  64%  73-153 SLWIGDLQFVVMDEQ 524  70% 720.2.1 (215/335) YIQNCFAHTGEVAS (57/81) VKVIRNKQSGQSEG YGFVEFISHAAAERN LQTYNGSMMPNSEQ PFRLNWASLG 48 Sl/Solyc07g064  67%  82-162 SLWIGDLQYWMDES 513  69% 510.2.1 (218/324) YLSTCFYHTGELVS (56/81) AKVIRNKQSGQSEG YGFLEFRSHAAAET VLQTYNGALMPNVE QNFRMNWASLG 62 Gm/Glyma13g2  64%  67-147 TLWIGDLQYWMDE 520  69% 7570.1 (214/331) NYLYTCFAHTGEVT (56/81) SVKVIRNKQTSQSEG YGFIEFNSRAGAERI LQTYNGAIMPNGGQ SFRLNWATFS 24 Os/LOC_Os08g  63%  96-174 TLWIGDLQYWMDE 501  69% 09100.1 (206/325) NYISACFAPTGELQS (56/81) VKLIRDKQTGQLQG YGFIEFTSHAGAERV LQTYNGAMMPNVE QTYRLNWAS 54 Pt/POPTR_000  61%  78-158 TLWIGDLQYWMDE 516  69% 4s01690.1 (213/349) NYIASCFAHTGEVAS (56/81) VKIIRNKQTSQIEGY GFIEMTSHGAAERIL QTYNGTPMPNGEQN FRLNWASFS 52 At/AT1G11650.2  63%  63-144 TLWIGDLQYWMDE 515  68% (206/325) NFLYGCFAHTGEMV (56/82) SAKVIRNKQTGQVE GYGFIEFASHAAAER VLQTFNNAPIPSFPD QLFRLNWASLS 60 Gm/Glyma17g0  66%  66-146 TLWIGDLQYWMDE 519  67% 1800.1 (218/327) NYLYTCFAHTGELA (55/81) SVKVIRNKQTSQSEG YGFIEFTSRAGAERV LQTYNGTIMPNGGQ NFRLNWATFS 64 Gm/Glyma15g1  64%  68-148 TLWIGDLQYWMDE 521  67% 1380.1 (215/333) NYLYTCFAHTGEVS (55/81) SVKVIRNKQTSQSEG YGFIEFNSRAGAERI LQTYNGAIMPNGGQ SFRLNWATFS 38 Zm/GRMZM2  68%  71-151 TLWIGDLQYWMDE 508  66% G002874_T01 (219/322) NYLYSCFSQAGEVIS (54/81) VKIIRNKQTGQPEGY GFIEFSNHAVAEQVL QNYNGQMMPNVNQ PFKLNWATSG 58 Gm/Glyma07g3  66%  62-142 TLWIGDLQYWMDE 518  66% 8940.1 (217/326) NYLYTCLAHTGEVA (54/81) SVKVIRNKQTSQSEG YGFIEFTSRAGAERV LQTYNGTIMPNGGQ NFRLNWATLS 50 Eg/Eucgr.F034  69%  65-145 SLWIGDLQPHMDET 514  65% 62.1 (226/323) YLLNCFAHSGEVLS (53/81) AKVIRNKQTALPEG YGFIEFMTRAAAERI LQTYNGTLMPNSDQ NFRLNWATLG 36 Os/LOC_Os03g  67%  68-148 TLWIGDLQFWMEEN 507  65% 37270.1 (218/323) YLYNCFSQAGELISA (53/81) KIIRNKQTGQPEGYG FIEFGSHAIAEQVLQ GYNGQMMPNGNQV FKLNWATSG 56 Eg/Eucgr.D013  63%  93-171 TLWIGDLQYWMDE 517  64% 10.1 (193/303) AYLGTCFAATGEVA (52/81) NVKVIRNKQTMQPE GYGFIEFYTRAAAER VLQTYNGAIMPNGG QSFRLNWAS 26 Zm/GRMZM2  62% 122-200 TLWIGDLQYWMDD 250  62% G426591_T01 (204/324) NYIYGCFASTGEVQ (51/81) NVKLIRDKHTGQLQ GYGFIEFISRAAAER VLQTYNGTMMPNV ELPFRLNWAS 22 Bd/Bradi3g151  56%  99-177 TLWIGDLQYWMDE 500  61% 80.1 (213/376) NYVYGCFAHTGEVQ (50/81) SVKLIRDKQTGQLQ GYGFVEFTTRAGAE RVLQTYNGATMPN VEMPYRLNWAS 16 Bd/Bradi5g224  61%  89-167 TLWIGDLQYWMDE 497  60% 10.1 (201/327) TYIHGCFASTGELQS (49/81) VKLIRDKQTGQLQG YGFVEFTSHAAAER VLQGYNGHAMPNV DLAYRLNWAS 30 Os/LOC_Os07g  58% 129-210 SLWIGDLQYWMDES 504  59% 33330.1 (205/348) YLSNAFAPMGQQVT (49/82) SVKVIRNKQSGHSE GYGFIEFQSHAAAE YALANFNGRMMLN VDQLFKLNWASSG 18 Zm/GRMZM2  58%  93-171 TLWIGDLQYWMDE 498  59% G012628_T01 (191/329) NYVFGCFSNTGEVQ (48/81) NVKLIRDKNSGQLQ GYGFVEFTSRAAAE RVLQTYNGQMMPN VDLTFRLNWAS 20 Zm/GRMZM2  58%  87-165 TLWIGDLQYWMDD 499  58% G058098_T02 (192/331) NYVFGCFSNTGEVQ (47/81) NVKLIRDKNSGQLQ GYGFVEFTSRAAAE RVLQTYNGQMMPN VDLTFRLNWAS 32 Zm/GRMZM2  53% 115-197 TLWIGDLQHWMDE 505  57% G127510_T01 (191/354) NYLHYNAFAAVAQ (48/83) QIASVKIIRNKQTGH SEGYGFIEFYSRAAA EHTLMNFNGQMMP NVEMTFKLNWASAS 34 Zm/GRMZM2  55% 147-229 TLWIGDLQYWMDE 506  56% G169615_T01 (188/338) NYLHYNAFAPVAQQ (47/83) IASVKIIRNKQTGHS EGYGFIEFYSQAAAE HTLMNFNGQMMPNI EMAFKLNWASAS 28 Bd/Bradi1g262  55% 115-197 SLWIGDLQYWMDE 503  56% 10.1 (181/324) AYLHNAFAPMGPQQ (47/83) VASVKIIRNKQTGQP EGYGFIEFHSRAAAE YALASFNGHAMPNV DLPFKLNWASAS

TABLE 5 Conserved ‘RRM2 domain’ of RBP45A and closely related sequences Col. 7 Percent identity Col. 3 Col. 4 of RRM2 Percent RRM2 Col. 6 domain Col. 1 identity of domain SEQ ID in Col. 5 to SEQ Col. 2 polypeptide in amino Col. 5 NO: of RRM2 ID Species/ in Col. 1 to acid Conserved RRM2 RRM2 domain of NO: Identifier RBP45A coordinates domain domain RBP45A 42 At/RBP45A or 100% 153-232 DHTIFVGDLAPEVTD 538 100% AT5G54900.1 (387/387) YMLSWITKNVYGSV (80/80) KGAKVVLDRTTGRS KGYGFVRFADENEQ MRAMTEMNGQYCS TRPMRIGPAA 40 At/AT4G27000.1  71% 172-251 EHTVFVGDLAPDVT 537  83% (282/394) DHMLTETFKAVYSS (67/80) VKGAKVVNDRTTG RSKGYGFVRFADES EQIRAMTEMNGQYC SSRPMRTGPAA 44 Pt/POPTR_000  70% 159-238 DYTVFIGDLAADVN 539  82% 1s45000.1 (228/323) DYLLQETFRNVYSS (66/80) VKGAKVVTDRVTG RSKGYGFVRFADEN EQMRAMVEMNGQY CSTRPMRIGPAA 46 Pt/POPTR_001  69% 162-241 DFTVFVGDLAADVN 540  81% 1s14150.1 (231/331) DYLLQETFRNVYPS (65/80) VKGAKVVTDRVTG RSKGYGFIRFADENE QRRAMVEMNGQYC STRPMRIGPAA 50 Eg/Eucgr.F034  69% 156-235 DYTIFVGDLAADVT 542  78% 62.1 (226/323) DHMLQETFRAHYPS (63/80) VKGAKIVIDRTTGRS KGYGFVRFGDETEQ LRAMTEMNGMYCS SRPMRIGPAA 38 Zm/GRMZM2  68% 162-241 DYTIFVGDLASDVT 536  77% G002874_T01 (219/322) DFILQDTFKSRYPSV (62/80) KGAKVVFDRTTGRS KGYGFVKFADSDEQ TRAMTEMNGQYCSS RAMRLGPAS 36 Os/LOC_Os03g  67% 159-238 DYTIFVGDLASDVT 535  77% 37270.1 (218/323) DLILQDTFKAHYQS (62/80) VKGAKVVFDRSTGR SKGYGFVKFGDLDE QTRAMTEMNGQYC SSRPMRIGPAS 52 At/AT1G11650.2  63% 154-233 DYTIFVGDLAADVT 543  77% (206/325) DYILLETFRASYPSV (62/80) KGAKVVIDRVTGRT KGYGFVRFSDESEQI RAMTEMNGVPCSTR PMRIGPAA 48 Sl/Solyc07g064  67% 172-251 EYTIFVGDLAADVT 541  76% 510.2.1 (218/324) DYVLQETFKPVYSS (61/80) VKGAKVVTDRITGR TKGYGFVKFSDESE QLRAMTEMNGVLC SSRPMRIGPAA 70 Sl/Solyc03g031  64% 164-243 EYTIFVGDLAADVT 552  76% 720.2.1 (215/335) DYMLQETFRANYPS (61/80) VKGAKVVTDRVTG RTKGYGFVKFADES EQLHAMTEMNGKF CSTRPMRIGPAA 66 Sl/So1yc02g080  66% 171-250 EYTIFVGDLAADVS 550  75% 420.2.1 (216/325) DYMLQETFRANYPS (60/80) VKGAKVVTDKATG RTKGYGFVKFGDES EQLRAMTEMNGQF CSTRPMRIGPAA 58 Gm/Glyma07g3  66% 153-232 DHTIFVGDLAADVT 546  75% 8940.1 (217/326) DYLLQETFRARYPSI (60/80) KGAKVVIDRLTGRT KGYGFVRFGDESEQ VRAMTEMQGVLCS TRPMRIGPAS 68 Sl/Solyc10g005  65% 168-247 EYTIFVGDLAADVT 551  75% 260.2.1 (218/333) DYMLQETFRPNYPSI (60/80) KGAKVVTDRATGH TKGYGFVRFGDESE QLRAMTEMNGKFCS TRPMRIGPAA 62 Gm/Glyma13g2  64% 159-238 DYTIFVGDLAADVT 548  75% 7570.1 (214/331) DYLLQETFRARYNS (60/80) VKGAKVVIDRLTGR TKGYGFVRFSDESE QVRAMTEMQGVLC STRPMRIGPAS 64 Gm/Glyma15g1  64% 160-239 DYTIFVGDLAADVT 549  75% 1380.1 (215/333) DYLLQETFRARYNS (60/80) VKGAKVVIDRLTGR TKGYGFVRFSEESEQ MRAMTEMQGVLCS TRPMRIGPAS 60 Gm/Glyma17g0  66% 157-236 DHTIFVGDLAADVT 547  73% 1800.1 (218/327) DYLLQETFRARYPS (59/80) AKGAKVVIDRLTGR TKGYGFVRFGDESE QVRAMSEMQGVLC STRPMRIGPAS 30 Os/LOC_Os07g  58% 222-301 EHTIFVGDLASDVTD 532  73% 33330.1 (205/348) SMLEEAFKTSYPSVR (59/80) GAKVVFDKVTGRSK GYGFVRFGDENEQT RAMTEMNGATLSTR QMRLGPAA 24 Os/LOC_Os08g  63% 184-263 DYTIFVGDLAADVT 529  72% 09100.1 (206/325) DYILQETFRVHYPSV (58/80) KGAKVVTDKMTMR SKGYGFVKFGDPSE QARAMTEMNGMVC SSRPMRIGPAA 26 Zm/GRMZM2  62% 210-289 DYTIFVGDLAADVT 530  72% G426591_T01 (204/324) DYVLQETFRAHYPS (58/80) VKGAKVVTDKLTM RTKGYGFVKFGDPN EQARAMTEMNGML CSSRPMRIGPAA 16 Bd/Bradi5g224  61% 177-256 DYTIFVGDLAADVT 525  72% 10.1 (201/327) DYILQETFRVHYPSV (58/80) KGAKVVTDKMTMR SKGYGFVKFGDPTE QARAMTEMNGMPC SSRPMRIGPAA 54 Pt/POPTR_000  61% 168-247 DFTIFVGDLAADVT 544  72% 4s01690.1 (213/349) DFMLQETFRAHFPS (58/80) VKGAKVVIDRLTGR TKGYGFVRFGDESE QLRAMTEMNGAFCS TRPMRVGLAS 22 Bd/Bradi3g151  56% 187-266 DYTIFVGDLAADVT 528  72% 80.1 (213/376) DYILQETFRVHYPSV (58/80) KGAKVVTDKLTMR SKGYGFVKFSDPIE QTRAMTEMNGMVC SSRPMRIGPAA 34 Zm/GRMZM2  55% 240-319 DHAIFVGDLAPDVT 534  72% G169615_T01 (188/338) DSMLEDVFRANYPS (58/80) VRGAKVVVDRITGR PKGYGFVHFGDLNE QARAMTEMNGMML STRKMRIGAAA 28 Bd/Bradi1g262  55% 208-287 DHTIFVGDLASDVT 531  72% 10.1 (181/324) DSMLQEIFKASYPSV (58/80) RGANVVTDRATGRS KGYGFVRFGDVNEQ TRAMTEMNGVTLSS RQLRIGPAA 20 Zm/GRMZM2  58% 175-254 DYTIFVGDLAADVT 527  71% G058098_T02 (192/331) DYLLQETFRVHYPS (57/80) VKGAKVVTDKLTM RTKGYGFVKFGDPT EQARAMTEMNGMP CSSRPMRIGPAA 18 Zm/GRMZM2  58% 181-260 EYTIFVGDLAADVT 526  70% G012628_T01 (191/329) DYLLQETFRVHYPS (56/80) VKGAKVVTDKLTM RTKGYGFVKFGDPT EQARAMTEMNGMP CSSRPMRIGPAA 32 Zm/GRMZM2  53% 208-287 DRTIFVGDLAHDVT 533  68% G127510_T01 (191/354) DSMLEDVFRAKYPS (55/80) VRGANVVVDRMTG WPKGFGFVRFGDLN EQARAMTEMNGML LSTRQMRIGAAA 56 Eg/Eucgr.D013  63% 182-261 DYTIFVGDLASDVT 545  67% 10.1 (193/303) DYMLQEMFRGRYPS (54/80) VRSAKVVMDRLTSR TKGYGFVKFGDESE QIRAMSEMNGVFLS TRPMRIGLAT

TABLE 6 Conserved ‘RRM3 domain’ of RBP45A and closely related sequences Col. 7 Percent identity Col. 3 Col. 4 of RRM3 Percent RRM3 Col. 6 domain Col. 1 identity of domain SEQ ID in Col. 5 to SEQ Col. 2 polypeptide in amino Col. 5 NO: of RRM3 ID Species/ in Col. 1 to acid Conserved RRM3 RRM3 domain of NO: Identifier RBP45A coordinates domain domain RBP45A 42 At/RBP45A or 100% 260-332 TTIFVGGLDANVTD 566 100% AT5G54900.1 (387/387) DELKSIFGQFGELLH (73/73) VKIPPGKRCGFVQY ANKASAEHALSVLN GTQLGGQSIRLSWG RS 40 At/AT4G27000.1  71% 278-350 TTIFVGAVDQSVILD 565  83% (282/394) DLKSVFGQFGELVH (61/73) VKIPAGKRCGFVQY ANRACAEQALSVLN GTQLGGQSIRLSWG RS 50 Eg/Eucgr.F034  69% 265-337 TTIFVGGLDPSVSDD 570  75% 62.1 (226/323) LLRQVFSQYGELHH (55/73) VKIPPGKRCGFVQFT SRACAEQALLMLNG TQLGGQSIRLSWGR S 38 Zm/GRMZM2  68% 271-343 TTVFVGGLDPSVTD 564  75% G002874_T01 (219/322) ELLKQTFSPYGELLY (55/73) VKIPVGKRCGFVQY SNRASAEEAIRVLNG SQLGGQSIRLSWGRS 66 Sl/Solyc02g080  66% 278-350 TTIFVGNLDSNITDE 578  73% 420.2.1 (216/325) HLRQIFGHYGQLLH (54/73) VKIPVGKRCGFIQFA DRSCAEEALRVLNG TQLGGQSIRLSWGR S 60 Gm/Glyma17g0  66% 265-337 TTIFVGNLDPNVTDD 575  73% 1800.1 (218/327) HLRQVFGQYGELVH (54/73) VKIPAGKRCGFVQF ADRSCAEEALRVLN GTLLGGQNVRLSWG RS 70 Sl/Solyc03g031  64% 271-343 TTIFVGNLDANVTD 580  73% 720.2.1 (215/335) DHLRQVFGNYGQLL (54/73) HVKIPVGKRCGFVQ FADRSCAEEALRAL SGTQLGGQTIRLSW GRS 46 Pt/POPTR_001  69% 270-342 TTIFVGALDPSVTDD 568  72% 1s14150.1 (231/331) TLRAVFSKYGELVH (53/73) VKIPAGKRCGFVQF ANRTSAEQALSMLN GTQIAGQNIRLSWG RS 36 Os/LOC_Os03g  67% 268-340 TTVFVGGLDPSVTD 563  72% 37270.1 (218/323) EVLKQAFSPYGELV (53/73) YVKIPVGKRCGFVQ YSNRASAEEAIRML NGSQLGGQSIRLSW GRS 58 Gm/Glyma07g3  66% 261-333 TTIFVGNLDPNVTDD 574  72% 8940.1 (217/326) HLRQVFGHYGELVH (53/73) VKIPAGKRCGFVQF ADRSCAEEALRVLN GTLLGGQNVRLSWG RS 62 Gm/Glyma13g2  64% 269-341 TTIFVGNLDPNVTDD 576  72% 7570.1 (214/331) HLRQVFSQYGELVH (53/73) VKIPAGKRCGFVQF ADRSCAEEALRVLN GTLLGGQNVRLSWG RS 64 Gm/Glyma15g1  64% 270-342 TTIFVGNLDPNVTDD 577  72% 1380.1 (215/333) HLRQVFSQYGELVH (53/73) VKIPAGKRCGFVQF ADRSCAEEALRVLN GTLLGGQNVRLSWG RS 56 Eg/Eucgr.D013  63% 291-363 KTVFVGGLDPNVTD 573  72% 10.1 (193/303) DHLRQVFGQYGEIV (53/73) QVKIPPGKRCGFVQF ADRSCAEEALRMLN GTQLGGQNIRLSWG RS 54 Pt/POPTR_000  61% 276-348 TTIFVGNLDSNVMD 572  72% 4s01690.1 (213/349) DHLKELFGQYGQLL (53/73) HVKIPAGKRCGFVQ FADRSSAEEALKML NGAQLSGQNIRLSW GRN 44 Pt/POPTR_000  70% 267-339 TTIFVGALDPSVTDD 567  71% 1s45000.1 (228/323) TLRAVFSKYGELVH (52/73) VKIPAGKRCGFVQF ANRTCAEQALSMLN GTQIAGQNIRLSWG RS 48 Sl/Solyc07g064  67% 279-351 TTIFVGGLDPSVAEE 569  71% 510.2.1 (218/324) HLRQVFSPYGELVH (52/73) VKIVAGKRCGFVQF GSRASAEQALSSLN GTQLGGQSIRLSWG RS 68 Sl/Solyc10g005  65% 274-346 TTIFVGNLDASVTDD 579  71% 260.2.1 (218/333) HLRQVFGNYGQLLH (52/73) VKIPLGKRCGFVQFT DRSCAEEALNALSG TQLGGQTIRLSWGR S 52 At/AT1G11650.2  63% 261-333 TTVFVGGLDASVTD 571  69% (206/325) DHLKNVFSQYGEIV (51/73) HVKIPAGKRCGFVQ FSEKSCAEEALRML NGVQLGGTTVRLSW GRS 26 Zm/GRMZM2  62% 315-387 TTIFVGGLDPNVILD 558  69% G426591_T01 (204/324) MLKQVFTPYGDVV (51/73) HVKIPVGKRCGFVQ YANRSSAEEALVILQ GTLVGGQNVRLSW GRS 24 Os/LOC_Os08g  63% 289-361 TTIFVGGLDPSVTDD 557  68% 09100.1 (206/325) MLKQVFTPYGDVV (50/73) HVKIPVGKRCGFVQ FANRASADEALVLL QGTLIGGQNVRLSW GRS 16 Bd/Bradi5g224  61% 284-356 TTIFVGGLDPNVILD 553  68% 10.1 (201/327) ALKQVFAPYGEVIH (50/73) VKIPVGKRCGFVQF VNRPSAEQALQMLQ GTPIGGQNVRLSWG RS 22 Bd/Bradi3g151  56% 293-365 TTIFVGGLDPNVILD 556  68% 80.1 (213/376) MLKQVFAPYGEVV (50/73) HVKIPVGKRCGFVQ YASRSSSEEALLML QGTVIGGQNVRLSW GRS 30 Os/LOC_Os07g  58% 332-404 TTIFVGGLDSNVNED 560  64% 33330.1 (205/348) HLKQVFTPYGEIGY (47/73) VKIPLGKRCGFVQFT SRSSAEEAIRVLNGS QIGGQQVRLSWGRT 18 Zm/GRMZM2  58% 288-360 TTIFVGGLDPNVILD 554  64% G012628_T01 (191/329) TLKQVFSPYGEVVH (47/73) VKIPVGKRCGFVQF VTRPSAEQALLMLQ GALIGAQNVRLSWG RS 20 Zm/GRMZM2  58% 282-354 TTIFVGGLDPNVILD 555  64% G058098_T02 (192/331) VLKQAFSPYGEVIH (47/73) VKIPVGKRCGFVQF VTRPSAEQALLMLQ GALIGAQNVRLSWG RS 34 Zm/GRMZM2  55% 351-423 TTVFVGGLDSNVDE 562  58% G169615_T01 (188/338) EYLRQIFTPYGEISY (43/73) VKIPVGKHCGFVQF TSRSCAEEAIQMLN GSQIGGQKARLSWG RS 32 Zm/GRMZM2  53% 319-391 TTVFVGGLDSNVNE 561  58% G127510_T01 (191/354) EYLRQIFTPYGEISY (43/73) VKIPVGKHCGFVQF TSRSCAEEAIRMLNG SQVGGQKVRLSWG RS 28 Bd/Bradi1g262  55% 320-392 TTIFVGGLDSNIDEN 559  57% 10.1 (181/324) YLRQVFTPYGEVGY (42/73) VKIPVGKRCGFVQF TSRSCAEEAINALNG TPIGGNNVRLSWGR S

These functionally-related and/or closely-related RBP45A clade polypeptides may be identified by a consensus first RRM domain (RRM1 domain) sequence, SEQ ID NO: 844:

X¹LWIGDLQX⁹X¹⁰MX¹²X¹³X¹⁴X¹⁵X¹⁶X¹⁷X¹⁸X¹⁹X²⁰X²¹X²²X²³X²⁴X²⁵X²⁶X²⁷X²⁸X²⁹X³⁰X³¹X³²KX³⁴I RX³⁷KX³⁹X⁴⁰X⁴¹X⁴²X⁴³X⁴⁴GYGFX⁴⁹EX⁵¹X⁵²X⁵³X⁵⁴X⁵⁵X⁵⁶AEX⁵⁹X⁶⁰LX⁶²X⁶³X⁶⁴NX⁶⁶X⁶⁷X⁶⁸X⁶⁹X⁷⁰X⁷¹X⁷²X⁷³X⁷⁴X⁷⁵X⁷⁶X⁷⁷X⁷⁸X⁷⁹NWAX⁸³X⁸⁴X⁸⁵

where X¹=S or T; X⁹=any amino acid; X¹⁰=H or W; X¹²=D or E; X¹³=D or E; X¹⁴=any amino acid; X¹⁵=F or Y; X¹⁶=I, L, V or M; X¹⁷=H or absent; X¹⁸=any amino acid; X¹⁹=any amino acid; X²⁰=any amino acid; X²¹=F, I, L, V or M; X²²=any amino acid; X²³=any amino acid; X²⁴=any amino acid; X²⁵=A or G; X²⁶=P or absent; X²⁷=Q or absent; X²⁸=E or Q; X²⁹=any amino acid; X³⁰=any amino acid; X³¹=any amino acid; X³²=any amino acid; X³⁴=I, L, V or M; X³⁷=N or D; X³⁹=any amino acid; X⁴⁰=any amino acid; X⁴¹=any amino acid; X⁴²=any amino acid; X⁴³=any amino acid; X⁴⁴=E or Q; X⁴⁹=I, L, V or M; X⁵¹=F, I, L, V or M; X⁵²=any amino acid; X⁵³=any amino acid; X⁵⁴=H, Q or R; X⁵⁵=A, S or G; X⁵⁶=any amino acid; X⁵⁹=any amino acid; X⁶⁰=any amino acid; X⁶²=any amino acid; X⁶³=any amino acid; X⁶⁴=F or Y; X⁶⁶=any amino acid; X⁶⁷=any amino acid; X⁶⁸=any amino acid; X⁶⁹=I, L, V or M; X⁷⁰=any amino acid; X⁷¹=any amino acid; X⁷²=any amino acid; X⁷³=P or absent; X⁷⁴=any amino acid; X⁷⁵=any amino acid; X⁷⁶=any amino acid; X⁷⁷=F or Y; X⁷⁸=K or R; X⁷⁹=I, L, V or M; X⁸³=any amino acid or absent; X⁸⁴=any amino acid or absent; and X⁸⁵=S or G.

These functionally-related and/or closely-related RBP45A clade polypeptides also may be identified by a consensus second RRM domain (RRM2 domain) sequence, SEQ ID NO: 845:

X¹X²X³X⁴FX⁶GDLAX¹¹X¹²VX¹⁴DX¹⁶X¹⁷LX¹⁹X²⁰X²¹FX²³X²⁴X²⁵X²⁶X²⁷SX²⁹X³⁰X³¹AX³³X³⁴VX³⁶D X³⁸X³⁹TX⁴¹X⁴²X⁴³KGX⁴⁶GFX⁴⁹X⁵⁰FX⁵²X⁵³X⁵⁴X⁵⁵EQX⁵⁸X⁵⁹AMX⁶²EMX⁶⁵GX⁶⁷X⁶⁸X⁶⁹SX⁷¹RX⁷³X⁷⁴RX⁷⁶GX⁷⁸AX⁸⁰

where X¹=E or D; X²=any amino acid; X³=A or T; X⁴=I, L, V or M; X⁶=I, L, V or M; X¹¹=any amino acid; X¹²=E or D; X¹⁴=any amino acid; X¹⁶=any amino acid; X¹⁷=I, L, V or M; X¹⁹=any amino acid; X²⁰=E or D; X²¹=any amino acid; X²³=K or R; X²⁴=any amino acid; X²⁵=any amino acid; X²⁶=F or Y; X²⁷=any amino acid; X²⁹=any amino acid; X³⁰=K or R; X³¹=S or G; X³³=Nor K; X³⁴=I, L, V or M; X³⁶=any amino acid; X³⁸=K or R; X³⁹=any amino acid; X⁴¹=any amino acid; X⁴²=any amino acid; X⁴³=any amino acid; X⁴⁶=F or Y; X⁴⁹=I, L, V or M; X⁵⁰=any amino acid; X⁵²=A, S or G; X⁵³=E or D; X⁵⁴=any amino acid; X⁵⁵=any amino acid; X⁵⁸=any amino acid; X⁵⁹=any amino acid; X⁶²=any amino acid; X⁶⁵=N or Q; X⁶⁷=any amino acid; X⁶⁸=any amino acid; X⁶⁹=any amino acid; X⁷¹=S or T; X⁷³=any amino acid; X⁷⁴=I, L, V or M; X⁷⁶=any amino acid; X⁷⁸=any amino acid; and X⁸⁰=A, S or T.

These functionally-related and/or closely-related RBP45A clade polypeptides also may be identified by a consensus third RRM domain (RRM3 domain) sequence, SEQ ID NO: 846:

X¹TX³FVGX⁷X⁸DX¹⁰X¹¹X¹²X¹³X¹⁴X¹⁵X¹⁶LX¹⁸X¹⁹X²⁰FX²²X²³X²⁴GX²⁶X²⁷X²⁸X²⁹VKIX³³X³⁴GKX³⁷CGFX⁴¹QX⁴³X⁴⁴X⁴⁵X⁴⁶X⁴⁷X⁴⁸X⁴⁹X⁵⁰X⁵¹AX⁵³X⁵⁴X⁵⁵LX⁵⁷GX⁵⁹X⁶⁰X⁶¹X⁶²X⁶³X⁶⁴X⁶⁵X⁶⁶RLSWGRX⁷³

where X¹=any amino acid; X³=I, L, V or M; X⁷=any amino acid; X⁸=I, L, V or M; X¹⁰=any amino acid; X¹¹=any amino acid; X¹²=I, L, V or M; X¹³=any amino acid; X¹⁴=E or D; X¹⁵=N, E or D; X¹⁶=any amino acid; X¹⁸=K or R; X¹⁹=any amino acid; X²⁰=any amino acid; X²²=any amino acid; X²³=any amino acid; X²⁴=F or Y; X²⁶=E, Q or D; X²⁷=I, L, V or M; X²⁸=any amino acid; X²⁹=any amino acid; X³³=any amino acid; X³⁴=any amino acid; X³⁷=any amino acid; X⁴¹=I, L, V or M; X⁴³=F or Y; X⁴⁴=any amino acid; X⁴⁵=any amino acid; X⁴⁶=K or R; X⁴⁷=any amino acid; X⁴⁸=S or C; X⁴⁹=A or S; X⁵⁰=E or D; X⁵¹=any amino acid; X⁵³=I, L, V or M; X⁵⁴=any amino acid; X⁵⁵=any amino acid; X⁵⁷=any amino acid; X⁵⁹=any amino acid; X⁶⁰=any amino acid; X⁶¹=I, L, V or M; X⁶²=S, A or G; X⁶³=A or G; X⁶⁴=any amino acid; X⁶⁵=any amino acid; X⁶⁶=any amino acid; and X⁷³=any amino acid. TCP6 Clade Polypeptides

TABLE 7 Conserved ‘TCP domain’ of TCP6 and closely related sequences Col. 7 Percent identity Col. 3 Col. 4 of TCP Percent TCP Col. 6 domain Col. 1 identity of domain SEQ ID in Col. 5 to SEQ Col. 2 polypeptide in amino Col. 5 NO: of TCP ID Species/ in Col. 1 to acid Conserved TCP TCP domain of NO: Identifier TCP6 coordinates domain domain TCP6 86 At/TCP6 or 100%  64-125 KKKPNKDRHLKVEG 588 100% AT5G41030.1 (243/243) RGRRVRLPPLCAARI (62/62) YQLTKELGHKSDGE TLEWLLQHAEPSILS ATVN 106 Sl/Solyc02g094  76% 33-94 KRKSNKDRHTKVEG 598 75% 290.1.1 (48/63) RGRRIRMPALCAARI (47/62) FQLTRELGHKSDGE TIQWLLQKAEPSIIA ATGH 96 Gm/Glyma16g0  48%  68-129 KRSSNKDRHTKVEG 593 74% 5840.1  (67/138) RGRRIRMPALCAARI (46/62) FQLTRELGHKSDGE TIQWLLQQAEPSIIA ATGT 84 At/AT3G27010.1  41%  74-135 KRSSNKDRHTKVEG 587 74% (128/311) RGRRIRMPALCAARI (46/62) FQLTRELGHKSDGE TIQWLLQQAEPSIIA ATGS 94 Pt/POPTR_001  37%  83-144 KRSSNKDRHTKVEG 592 74% 7s09820.1 (113/300) RGRRIRMPALCAARI (46/62) FQLTRELGHKSDGE TIQWLLQQAEPSIIA ATGT 88 Cc/clementine0.  36%  66-127 KRSSNKDRHTKVEG 589 74% 9_016144m (114/312) RGRRIRMPALCAARI (46/62) FQLTRELGHKSDGE TIQWLLQQAEPSIIA ATGT 90 Cc/clementine0.  36%  66-127 KRSSNKDRHTKVEG 590 74% 9_016174m (114/312) RGRRIRMPALCAARI (46/62) FQLTRELGHKSDGE TIQWLLQQAEPSIIA ATGT 92 Pt/POPTR_000  34%  78-139 KRSSNKDRHTKVEG 591 74% 1s33470.1 (115/332) RGRRIRMPALCAARI (46/62) FQLTRELGHKSDGE TIQWLLQQAEPSIIA ATGT 98 Gm/Glyma19g2  34%  68-129 KRSSNKDRHTKVEG 594 74% 6560.1 (100/290) RGRRIRMPALCAARI (46/62) FQLTRELGHKSDGE TIQWLLQQAEPSIIA ATGT 100 Cc/clementine0.  38% 30-91 KRSSNKDRHKKVDG 595 73% 9_018374m  (95/245) RGRRIRMPALCAARI (45/62) FQLTRELGHKSDGE TIQWLLQQAEPSIIA ATGT 104 Pt/POPTR_000  35%  60-121 KRSSNKDRHKKVEG 597 72% 3s16630.1  (99/280) RGRRIRIPALCAARIF (45/62) QLTRELEHKSDGETI QWLLQQAEPSIIAAT GT 72 Bd/Bradi2g592  39%  84-145 KRSSNKDRHTKVDG 581 70% 40.1  (86/220) RGRRIRMPALCAARI (44/62)) FQLTRELGHKSDGE TVQWLLQQAEPAIV AATGS 74 Os/LOC_Os01g  39%  83-144 KRSSNKDRHTKVDG 582 70% 69980.1  (76/194) RGRRIRMPALCAARI (44/62) FQLTRELGHKSDGE TVQWLLQQAEPAIV AATGT 78 Zm/GRMZM2  38%  98-159 KRSSNKDRHTKVDG 584 70% G092214_T01  (85/218) RGRRIRMPALCAARI (44/62) FQLTRELGHKSDGE TVQWLLQQAEPAIV AATGT 80 Zm/GRMZM2  38%  98-159 KRSSNKDRHTKVDG 585 70% G092214_T02  (85/218) RGRRIRMPALCAARI (44/62)) FQLTRELGHKSDGE TVQWLLQQAEPAIV AATGT 76 Zm/GRMZM2  37%  88-149 KRSSNKDRHTKVDG 583 70% G034638_T01  (82/216) RGRRIRMPALCAARI (44/62) FQLTRELGHKSDGE TVQWLLQQAEPAIV AATGT 102 Pt/POPTR_000  36%  60-121 KRSSNKDRHKKVDG 596 70% 1s13500.1  (85/236) RGRRIRMPALCAARI (44/62) FQLTRELGNKSDGE TIQWLLQQAEPSIIA ATGT 82 Eg/Eucgr.B035  36%  40-101 KRSSNKDRHKKVDG 586 70% 29.1 (105/286) RGRRIRMPALCAARI (44/62) FQLTRELGHKTDGE TIQWLLQQAEPSIVA ATGT

These functionally-related and/or closely-related TCP6 clade polypeptides may be identified by a consensus TCP domain sequence, SEQ ID NO: 847:

KX²X³X⁴NKDRHX¹⁰KVX¹³GRGRRX¹⁹RX²¹PX²³LCAARIX³⁰QLTX³⁴ELX³⁷X³⁸KX⁴⁰DGETX⁴⁵X⁴⁶W LLQX⁵¹AEPX⁵⁵IX⁵⁷X⁵⁸ATX⁶¹X⁶²

where X²=K or R; X³=any amino acid; X⁴=S or P; X¹⁰=any amino acid; X¹³=D or E; X¹⁹=I, L, V or M; X²¹=I, L, V or M; X²³=A or P; X³⁰=F or Y; X³⁴=K or R; X³⁷=any amino acid; X³⁸=H or N; X⁴⁰=S or T; X⁴⁵=I, L, V or M; X⁴⁶=Q or E; X⁵¹=H, Q or K; X⁵⁵=S or A; X⁵⁷=I, L, V or M; X⁵⁸=S or A; X⁶¹=any amino acid; and X⁶²=any amino acid. PIL1 Clade Polypeptides

TABLE 8 Conserved ‘bHLH domain’ of PIL1 and closely related sequences Col. 7 Percent identity Col. 3 Col. 4 of bHLH Percent bHLH Col. 6 domain Col. 1 identity of domain SEQ ID in Col. 5 to SEQ Col. 2 polypeptide in amino Col. 5 NO: of bHLH ID Species/ in Col. 1 to acid Conserved bHLH bHLH domain of NO: Identifier PIL1 coordinates domain domain PIL1 108 At/PIL1 pr 100% 227-283 RKRSIEVHKLYER 599 100% AT2G46970.1 (416/416) KRRDEFNKKMRAL (57/57) QDLLPNCYKDDKA SLLDEAIKYMRTLQ LQVQ 112 Cc/clementine  41% 309-365 KKRTPEVHKRYER 601  70% 0.9_007946m  (96/231) KRRDKINKKMRAL (40/57) QELIPNCNKVDKAS VLEEAIDYLKTLQF QVM 116 Pt/POPTR_00  40% 379-435 RRRAIEIHNLSERK 603  70% 14s10700.1 (104/254) RRDRINKKMRALQ (40/57) DLIPNSNKVDKAS MLGEAIDYLKSLQL QVQ 114 Gm/Glyma10g  39% 187-243 RSRNAEVHNLCER 602  63% 27910.1 (104/262) KRRDKINKRMRILK (36/57) ELIPNCNKTDKASM LDDAIEYLKTLKLQ LQ 110 At/AT3G6209  43% 186-242 RKRNAEAYNSPER 600  61% 0.2 (173/399) NQRNDINKKMRTL (35/57) QNLLPNSHKDDNE SMLDEAINYMTNL QLQVQ

These functionally-related and/or closely-related PIL1 clade polypeptides may be identified by a consensus bHLH domain sequence, SEQ ID NO: 848:

X¹X²RX⁴X⁵EX⁷X⁸X⁹X¹⁰X¹¹ERX¹⁴X¹⁵RX¹⁷X¹⁸X¹⁹NKX²²MRX²⁵LX²⁷X²⁸LX³⁰PNX³³X³⁴KX³⁶DX³⁸X³⁹SX⁴¹LX⁴³X⁴⁴AIX⁴⁷YX⁴⁹X⁵⁰X⁵¹LX⁵³X⁵⁴QX⁵⁶X⁵⁷

where X¹=R or K; X²=any amino acid; X⁴=any amino acid; X⁵=any amino acid; X⁷=any amino acid; X⁸=H or Y; X⁹=N or K; X¹⁰=any amino acid; X¹¹=any amino acid; X¹⁴=N or K; X¹⁵=any amino acid; X¹⁷=D or N; X¹⁸=any amino acid; X¹⁹=F, I, L, V or M; X²²=R or K; X²⁵=any amino acid; X²⁷=Q or K; X²⁸=N, D or E; X³⁰=I, L, V or M; X³³=S or C; X³⁴=any amino acid; X³⁶=any amino acid; X³⁸=N or K; X³⁹=any amino acid; X⁴¹=I, L, V or M; X⁴³=any amino acid; X⁴⁴=D or E; X⁴⁷=any amino acid; X⁴⁹=I, L, V or M; X⁵⁰=any amino acid; X⁵¹=any amino acid; X⁵³=Q or K; X⁵⁴=F, I, L, V or M; X⁵⁶=I, L, V or M; and X⁵⁷=any amino acid. PCL1 Clade Polypeptides

TABLE 9 Conserved ‘SANT domain’ of PCL1 and closely related sequences Col. 7 Percent identity Col. 3 Col. 4 of SANT Percent SANT Col. 6 domain Col. 1 identity of domain SEQ ID in Col. 5 to SEQ Col. 2 polypeptide in amino Col. 5 NO: of SANT ID Species/ in Col. 1 to acid Conserved SANT SANT domain of NO: Identifier PIL1 coordinates domain domain PIL1 126 At/PCL1 or 100% 146-196 RLVWTPQLHKRFVD 608 100% AT3G46640.3 (324/324) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 128 At/AT5G59570.1  63% 143-193 RLVWTPQLHKRFVD 609 100% (181/286) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 148 Gm/Glyma11g1  62% 146-196 RLVWTPQLHKRFVD 619 100% 4490.1 (156/249) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 150 Gm/Glyma11g1  62% 146-196 RLVWTPQLHKRFVD 620 100% 4490.2 (156/249) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 152 Gm/Glyma12g0  60% 145-195 RLVWTPQLHKRFVD 621 100% 6410.1 (148/245) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 144 Sl/Solyc06g005  59% 148-198 RLVWTPQLHKRFVD 617 100% 680.2.1 (145/242) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 130 Cc/clementine0.  58% 158-208 RLVWTPQLHKRFVD 610 100% 9_013078m (146/251) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 132 Cc/clementine0.  58% 158-208 RLVWTPQLHKRFVD 611 100% 9_013095m (146/251) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 134 Cc/clementine0.  58% 158-208 RLVWTPQLHKRFVD 612 100% 9_013088m (146/251) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 136 Eg/Eucgr.B023  53% 170-220 RLVWTPQLHKRFVD 613 100% 13.1 (150/281) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 124 Si/Si002653m  47% 129-179 RLVWTPQLHKRFVD 607 100% (137/291) VVAHLGIKNAVPKTI (51/51) MQLMNVEGLTREN VASHLQKYR 142 Pt/POPTR_000  56% 133-183 RLVWTPQLHKRFVD 616  98% 9s03990.2 (167/297) VVSHLGIKNAVPKTI (50/51) MQLMNVEGLTREN VASHLQKYR 154 Vv/GSVIVT01  54% 233-283 RLVWTPQLHKRFVD 622  98% 024916001 (160/291) VVGHLGIKNAVPKTI (50/51) MQLMNVEGLTREN VASHLQKYR 140 Pt/POPTR_000  53% 161-211 RLVWTPQLHKRFVD 615  98% 9s03990.1 (170/315) VVSHLGIKNAVPKTI (50/51) MQLMNVEGLTREN VASHLQKYR 120 Os/LOC_Os01g  55% 120-170 RLVWTPQLHKRFVE 605  96% 74020.1 (129/233) VVAHLGMKNAVPK (49/51) TIMQLMNVEGLTRE NVASHLQKYR 122 Zm/GRMZM2  51% 118-168 RLVWTPQLHKRFVD 606  96% G067702_T01 (118/229) VVAHLGIKKAVPKTI (49/51) MELMNVEGLTREN VASHLQKYR 146 Sl/Solyc06g076  53% 152-202 RLVWTPQLHKRFIE 618  94% 350.2.1 (129/241) VVAHLGIKGAVPKTI (48/51) MQLMNVEGLTREN VASHLQKYR 138 Pt/POPTR_000  50% 118-168 RLVWTPQLHKRFVD 614  94% 1s25040.1 (155/310) VVGHLGMKNAVPK (48/51) NVEGLTRE TIMQWM NVASHLQKYR 118 Bd/Bradi2g620  47% 116-166 RMVWNPQLHKRFV 604  94% 67.1 (142/301) DVVAHLGIKSAVPK (48/51) TIMQLMNVEGLTRE NVASHLQKYR

These functionally-related and/or closely-related PCL1 clade polypeptides may be identified by a consensus SANT domain sequence, SEQ ID NO: 849:

RX²VWX⁵PQLHKRFX¹³X¹⁴VVX¹⁷HLGX²¹KX²³AVPKTIMX³¹X³²MNVEGLTRENVASHLQKYR where X²=I, L, V, or M; X⁵=any amino acid; X¹³=I, L, V, or M; X¹⁴=D or E; X¹⁷=A, S or G; X²¹=I, L, V, or M; X²³=any amino acid; X³¹=Q or E; and X³²=any amino acid.

GTL1 Clade Polypeptides

TABLE 10 Conserved ‘Tribelix domain 1’ of GTL1 and closely related sequences Col. 7 Percent identity of trihelix Col. 3 Col. 4 domain 1 Percent Trihelix Col. 6 in Col. 5 Col. 1 identity of domain 1 SEQ ID to first SEQ polypeptide in amino Col. 5 NO: of trihelix ID Col. 2 in Col. 1 to acid Conserved trihelix trihelix domain of NO: Species/Identifier GTL1 coordinates domain 1 domain 1 GTL1 168 At/GTL1 or 100% 60-143 GNRWPREETLALLRI 629 100%  AT1G33240.1 (669/669) RSDMDSTFRDATLK (84/84) APLWEHVSRKLLEL GYKRSSKKCKEKFE NVQKYYKRTKETRG GRHDGKAYKFFSQ 156 At/GTL1 or 100% 60-143 GNRWPREETLALLRI 623 100%  G634 (152/152) RSDMDSTFRDATLK (84/84) APLWEHVSRKLLEL GYKRSSKKCKEKFE NVQKYYKRTKETRG GRHDGKAYKFFSQ 158 Bd/Bradi5g17150.1  72% 85-168 GNRWPREETLALIRI 624 82% (66/91) RSEMDATFRDATLK (69/84) GPLWEEVSRKLAEL GYKRNAKKCKEKFE NVHKYYKRTKEGRT GRQDGKSYRFFSE 166 Pt/POPTR_0001s45870.1 75% 104-187  GNRWPRQETLALLQ 628 80% (70/93) IRSEMDAAFRDATL (68/84) KGPLWEDVSRKLAE MGYKRSAKKCKEK FENVHKYYKRTKEG RAGRQDGKSYRFFS Q 172 Gm/Glyma20g30640.1  68% 63-146 GNRWPRQETLALLR 631 77%  (73/107) IRSDMDVAFRDASV (65/84) KGPLWEEVSRKMAE LGYHRSSKKCKEKF ENVYKYHKRTKEGR SGKQDGKTYRFFDQ 186 Gm/Glyma20g30650.1  75% 66-149 GNRWPRQETLALLK 638 76% (66/87) IRSDMDAVFRDSSL (64/84) KGPLWEEVARKLSE LGYHRSAKKCKEKF ENVYKYHKRTKESR SGKHEGKTYKFFDQ 162 Bd/Bradi3g30457.1  52% 86-169 GNRWPRQETLVLLK 626 76% (143/275) IRSDMDAAFRDATL (64/84) KGPLWEEVSRKLAE EGYRRNAKKCKEKF ENVHKYYKRTKDSR AGRNDGKTYRFFQQ 164 Si/Si034382m  63% 74-157 GNRWPRQETLALLK 627 75% (74/116) IRSEMDAAFREAAL (63/84) KGPLWEQVSRKLEA MGYKRSAKKCREKF ENVDKYYKRTKDG RAGRGDGKAYRFFS E 160 Zm/GRMZM2G169580_T01  58% 98-181 GNRWPREETLALIRI 625 75%  (80/136) RTEMDADFRNAPLK (63/84) APLWEDVARKLAGL GYHRSAKKCKEKFE NVHKYYKRTKDAH AGRQDGKSYRFFSQ 188 Pt/POPTR_0002s06900.1  71% 58-141 ANRWPRQETLALLK 639 73% (68/95) IRSDMDAVFRDSGL (62/84) KGPLWEEVSRKLAE LGYHRSAKKCKEKF ENVYKYHKRTKEGR TGKSEGKSYKFFDE 184 Gm/Glyma16g28240.1  41% 53-136 GNRWPRQETLALLK 637 73% (108/260) IRSDMDTVFRDSSLK (62/84) GPLWEEVSRKLAEL GYQRSAKKCKEKFE NVYKYNKRTKDNK SGKSHGKTYKFFDQ 190 Pt/POPTR_0005s21420.1  72% 61-144 ANRWPRQETLALLK 640 71% (63/87) IRSAMDAVFRDSSL (60/84) KGPLWEEVSRKLAE LGYHRSAKKCKEKF ENLYKYHKRTKEGR TGKSEGKTYKFFDE 178 Pt/POPTR_0001s31660.1  70% 40-23  GNRWPKQETLALLK 634 71% (64/91) IRSDMDVAFKDSGL (60/84) KAPLWEEVSKKLNE LGYNRSAKKCKEKF ENIYKYHRRTKEGR SGRPNGKTYRFEEQ 170 Pt/POPTR_0005s21410.1  44% 64-147 GSRWPRQETLALLKI 630 71% (117/262) RSGMDVAFRDASVK (60/84) GPLWEEVSRKLAEL GYNRSGKKCKEKFE NVYKYHKRTKDGR TGKQEGKTYRFFDQ 176 Sl/Solyc12g056510.1.1  40% 70-153 GNRWPRQETLALLK 633 70% (212/519) IRSEMDVVFKDSSLK (59/84) GPLWEEVSRKLAEL GYHRSAKKCKEKFE NVYKYHRRTKDGR ASKADGKTYRFFDQ 180 Pt/POPTR_0019s02650.1  69% 40-123 ANRWPKQETLALLE 635 69% (64/92) IRSDMDVAFRDSVV (58/84) KAPLWEEVSRKLNE LGYNRSAKKCKEKF ENIYKYHRRTKGSQ SGRPNGKTYRFIAEQ 174 Sl/Solyc04g071360.2.1  42% 58-141 GNRWPRQETIALLKI 632 69% (74/175) RSEMDVIFRDSSLKG (58/84) PLWEEVSRKMADLG FHRSSKKCKEKEEN VYKYHKRTKDGRA SKADGKNYRFFEQ 182 Sl/Solyc11g005380.1.1  69% 52-135 GNRWPHEETLALLK 636 66% (64/92) IRSEMDVAFRDSNL (56/84) KSPLWDEISRKMAE LGYNRNAKKCREKF ENIYKYHKRTKDGR SGRQTGKNYRFFEQ

TABLE 11 Conserved ‘Tribelix domain 2’ of GTL1 and closely related sequences Col. 7 Percent identity of trihelix Col. 3 Col. 4 domain 2 Percent Trihelix Col. 6 in Col. 5 Col. 1 identity of domain 2 SEQ ID to second SEQ polypeptide in amino Col. 5 NO: of trihelix ID Col. 2 in Col. 1 to acid Conserved trihelix trihelix domain of NO: Species/Identifier GTL1 coordinates domain 2 domain 2 GTL1 168 At/GTL1 or 100%  433-517 SSRWPKAEILALINL 647 100%  AT1G33240.1 (669/669) RSGMEPRYQDNVPK (85/85) GLLWEEISTSMKRM GYNRNAKRCKEKW ENINKYYKKVKESN KKRPQDAKTCPYFH R 156 At/GTL1 or 100%  187-259 SSRWPKAEILALINL 641 82% G634 (152/152) RSGMEPRYQDNVPK (70/85) GLLWEEISTSMKRM GYNRNAKRCKEKW ENINKYYKKVKESN NSN 166 Pt/POPTR_0001s45870.1 75% 520-604 SSRWPKPEVLALIKL 646 76% (70/93) RSGLETRYQEAGPK (65/85) GPLWEEISAGMLRL GYKRSSKRCKEKWE NINKYFKKVKESNK KRFEDAKTCPYFHE 172 Gm/Glyma20g30640.1 68% 457-541 SSRWPKVEVQALIK 649 76%  (73/107) LRTSMDEKYQENGP (65/85) KGPLWEEISASMKK LGYNRNAKRCKEK WENINKYFKKVKES NKRRPEDSKTCPYF HQ 174 Sl/Solyc04g071360.2.1 42% 459-543 SSRWPKAEVEALIKL 650 76%  (74/175) RTNLDVKYQENGPK (65/85) GPLWEEISSGMKKIG YNRNAKRCKEKWE NINKYFKKVKESNK KRPEDSKTCPYFHQ 158 Bd/Bradi5g17150.1 72% 496-580 SSRWPKTEVHALIQL 642 75% (66/91) RMDMDNRYQENGP (64/85) KGPLWEEISSGMRR LGYNRNPKRCKEK WENINKYFKKVKES NKRRPEDSKTCPYF HQ 162 Bd/Bradi3g30457.1 52% 453-537 SSRWPKAEVHALIQ 644 75% (143/275) LRSNLDTRYQEAGP (64/85) KGPLWEEISAGMRR MGYSRSSKRCKEK WENINKYFKKVKES NKKRPEDSKTCPYF HQ 176 Sl/Solyc12g056510.1.1 40% 455-539 SSRWPKEEIEALISLR 651 75% (212/519) TCLDLKYQENGPKG (64/85) PLWEEISSGMRKIGY NRNAKRCKEKWENI NKYFKKVKESNKKR PEDSKTCPYFHQ 164 Si/Si034382m 63% 458-542 PSRWPKAEVHALIQ 645 74%  (74/116) LRTELEARYQDSGP (63/85) KGPLWEDISAGMRR LGYNRSAKRCKEK WENINKYFKKVKES NKKRPEDSKTCPYY HQ 188 Pt/POPTR_0002s06900.1 71% 405-489 SSRWPKVEVQALIN 657 70% (68/95) LRANLDVKYQENG (60/85) AKGPLWEDISAGMQ KLGYNRSAKRCKEK WENINKYFKKVKES NKKRPEDSKTCPYF DQ 182 Sl/Solyc11g005380.1.1 69% 363-448 SSRWPKAEVEALIKL 654 70% (64/92) RTNVDLQYQDNGSS (61/86) KGPLWEDISCGMKK LGYDRNAKRCKEK WENINKYYRRVKES QKKRPEDSKTCPYF HQ 180 Pt/POPTR_0019s02650.1 69% 331-415 SSRWPKEEIESLIKIR 653 70% (64/92) TYLEFQYQENGPKG (60/85) PLWEEISTSMKNLG YDRSAKRCKEKWE NMNKYFKRVKDSN KKRPGDSKTCPYFQ Q 170 Pt/POPTR_0005s21410.1 44% 404-488 PSRWPKVEVEALIRI 648 70% (117/262) RTNLDCKYQDNGPK (60/85) GPLWEEISARMRKL GYNRNAKRCKEKW ENINKYFKKVKESK KKRPEDSKTCPYFQ Q 186 Gm/Glyma20g30650.1 75% 442-526 SSRWPKTEVHALIRL 656 69% (66/87) RTSLEAKYQENGPK (59/85) APFWEDISAGMLRL GYNRSAKRCKEKW ENINKYFKKVKESN KQRREDSKTCPYFH E 178 Pt/POPTR_0001s31660.1 70% 337-421 PSRWPKEEIEALIGL 652 69% (64/91) RTKLEFQYEENGPK (59/85) GPLWEEIS AS MKKL GYDRSAKRCKEKW ENMNKYFKRVKESN KRRPGDSKTCPYFQ Q 160 Zm/GRMZM2G169580_T01 58% 411-495 SSRWPKEEVEALIQV 643 68% (80/136) RNEKDEQYHDAGG (58/85) KGPLWEDIAAGMRR IGYNRSAKRCKEKW ENINKYYKKVKESN KRRPEDSKTCPYFH Q 190 Pt/POPTR_0005s21420.1 72% 406-490 SSRWPKVEVQALISL 658 67% (63/87) RADLDIKYQEHGAK (57/85) GPLWEDISAGMQKL GYNRSAKRCKEKW ENINKYFKKVKESN RKRPGDSKTCPYFD Q 184 Gm/Glyma16g28240.1 41% 412-496 SSRWPKAEVHALIRI 655 67% (108/260) RTSLETKYQENGPK (57/85) APLWEDISIAMQRL GYNRSAKRCKEKW ENINKYFKRVRESSK ERREDSKTCPYFHE

These functionally-related and/or closely-related GTL1 clade polypeptides may be identified by a consensus first Trihelix domain sequence (Trihelix 1), SEQ ID NO: 850:

X¹X²RWPX⁶X⁷ETX¹⁰X¹¹LX¹³X¹⁴IRX¹⁷X¹⁸MDX²¹X²²FX²⁴X²⁵X²⁶X²⁷X²⁸KX³⁰PLWX³⁴X³⁵X³⁶X³⁷X³⁸KX⁴⁰X⁴¹X⁴²X⁴³GX⁴⁵X⁴⁶RX⁴⁸X⁴⁹KKCX⁵³EKFENX⁵⁹X⁶⁰KYX⁶³X⁶⁴RTKX⁶⁸X⁶⁹X⁷⁰X⁷¹X⁷²X⁷³X⁷⁴X⁷⁵G KX⁷⁸YX⁸⁰FFX⁸³X⁸⁴

where X¹=A or G; X²=any amino acid; X⁶=any amino acid; X⁷=Q or E; X¹⁰=I, L, V or M; X¹¹=any amino acid; X¹³=I, L, V or M; X¹⁴=any amino acid; X¹⁷=S or T; X¹⁸=any amino acid; X²¹=any amino acid; X²²=any amino acid; X²⁴=R or K; X²⁵=N, D or E; X²⁶=A or S; X²⁷=any amino acid; X²⁸=I, L, V or M; X³⁰=A, S or G; X³⁴=D or E; X³⁵=any amino acid; X³⁶=I, L, V or M; X³⁷=A or S; X³⁸=RorK; X⁴⁰=I, L, V or M; X⁴¹=any amino acid; X⁴²=any amino acid; X⁴³=any amino acid; X⁴⁵=F or Y; X⁴⁶=H, Q, N, R or K; X⁴⁸=any amino acid; X⁴⁹=A, S or G; X⁵³=K or R; X⁵⁹=I, L, V or M; X⁶⁰=any amino acid; X⁶³=any amino acid; X⁶⁴=K or R; X⁶⁸=any amino acid; X⁶⁹=any amino acid; X⁷⁰=H, Q, K or, R; X⁷¹=any amino acid; X⁷²=S or G; X⁷³=R or K; X⁷⁴=any amino acid; X⁷⁵=any amino acid; X⁷⁸=any amino acid; X⁸⁰=R or K; X⁸³=any amino acid; and X⁸⁴=Q or E.

These functionally-related and/or closely-related GTL1 clade polypeptides may also be identified by a consensus first Trihelix domain sequence (Trihelix 2), SEQ ID NO: 851:

X¹SRWPKX⁷EX⁹X¹⁰X¹¹LIX¹⁴X¹⁵RX¹⁷X¹⁸X¹⁹X²⁰X²¹X²²YX²⁴X²⁵X²⁶X²⁷X²⁸X²⁹KX³¹X³²X³³WEX³⁶IX³⁸X³⁹X⁴⁰MX⁴²X⁴³X⁴⁴GYX⁴⁷RX⁴⁹X⁵⁰KRCKEKWENX⁶⁰NKYX⁶⁴X⁶⁵X⁶⁶VX⁶⁸X⁶⁹SX⁷¹X⁷²X⁷³X⁷⁴X⁷⁵X⁷⁶X⁷⁷X⁷⁸X⁷⁹X⁸⁰X⁸¹X⁸²X⁸³X⁸⁴X⁸⁵X⁸⁶

where X¹=S or P; X⁷=any amino acid; X⁹=I, L, V or M; X¹⁰=any amino acid; X¹¹=A or S; X¹⁴=any amino acid; X¹⁵=I, L, V or M; X¹⁷=any amino acid; X¹⁸=any amino acid; X¹⁹=any amino acid; X²⁰=E or D; X²¹=any amino acid; X²²=K, Q or R; X²⁴=any amino acid; X²⁵=E or D; X²⁶=any amino acid; X²⁷=any amino acid; X²⁸=S or absent; X²⁹=any amino acid; X³¹=A or G; X³²=any amino acid; X³³=F or L; X³⁶=E or D; X³⁸=A or S; X³⁹=any amino acid; X⁴⁰=any amino acid; X⁴²=any amino acid; X⁴³=N, K or R; X⁴⁴=I, L, V or M; X⁴⁷=any amino acid; X⁴⁹=any amino acid; X⁵⁰=A, S or P; X⁶⁰=I, L, V or M; X⁶⁴=F or Y; X⁶⁵=K or R; X⁶⁶=K or R; X⁶⁸=K or R; X⁶⁹=E or D; X⁷¹=any amino acid; X⁷²=N, K or R; X⁷³=any amino acid; X⁷⁴=N or R; X⁷⁵=any amino acid or absent; X⁷⁶=any amino acid or absent; X⁷⁷=D or absent; X⁷⁸=S, A or absent; X⁷⁹=K or absent; X⁸⁰=T or absent; X⁸¹=C or absent; X⁸²=P or absent; X⁸³=Y or absent; X⁸⁴=F, Y or absent; X⁸⁵=H, Q, D or absent; X⁸⁶=any amino acid or absent. DREB2H Clade Polypeptides

TABLE 12 Conserved ‘AP2 domain’ of DREB2H and closely related sequences Col. 7 Percent Col. 3 Col. 4 identity of Percent AP2 Col. 6 AP2 Col. 1 identity of domain in SEQ ID domain in SEQ polypeptide amino acid NO: of AP2 ID Col. 2 in Col. 1 to coordinates Col. 5 AP2 domain of NO: Species/Identifier DREB2H Col. 5 to Conserved AP2 domain domain DREB2H 218 At/DREB2H or 100%   65-122 CDYTGVRQRTVVGK 672 100%  AT2G40350.1 (157/157) WVAEIREPGRGAKL (58/58) WLGTFSSSYEAALA YDEASKAIYGQSAR LNL 192 At/G1755 100%   72-129 CDYTGVRQRTVVGK 659 100% (155/155) WVAEIREPGRGAKL (58/58) WLGTFSSSYEAALA YDEASKAIYGQSAR LNL 216 At/AT2G40340.1 86%  70-127 CDYRGVRQRRWGK 671 89% (108/125) WVAEIREPDGGARL (52/58) WLGTFSSSYEAALA YDEAAKAIYGQSAR LNL 232 Sl/Solyc05g052410.1.1 65%  72-129 CKYRGVRQRTWGK 679 75%  (82/125) WVAEIREPHRGRRL (44/58) WLGTFDTAIEAALA YDEAARAMYGPCA RLNL 230 Pt/POPTR_0010s19100.1 65%  78-135 CNYRGVRQRTWGK 678 75%  (79/121) WVAEIREPNRGPRL (44/58) WLGTFPTAYEAALA YDEAARAMYGPYA RLNV 226 Gm/Glymal4g06080.1 64%  78-135 CNYRGVRQRTWGK 676 75%  (80/125) WVGEIREPNRGSRL (44/58) WLGTFSSAQEAALA YDEAARAMYGPCA RLNF 224 Gm/Glyma02g42960.1 62%  78-135 CNYRGVRQRTWGK 675 75%  (79/127) WVGEIREPNRGSRL (44/58) WLGTFSSAQEAALA YDEAARAMYGPCA RLNF 228 Pt/POPTR_0008s07360.1 65%  78-135 CNYRGVRQRTWGK 677 74%  (79/121) WVAEIREPNRGPRL (43/58) WLGTFPTAYEAALA YDNAARAMYGSCA RLNI 234 Sl/Solyc06g050520.1.1 63%  80-137 CKYRGVRQRIWGK 680 72%  (79/125) WVAEIREPKRGSRL (42/58) WLGTFGTAIEAALA YDDAARAMYGPCA RLNL 214 Gm/Glymal3g38030.1 61%  63-120 CNYRGVRQRTWGK 670 72%  (76/123) WVAEIREPNRGNRL (42/58) WLGTFPTAIGAALA YDEAARAMYGSCA RLNF 208 Gm/Glyma06g45680.1 61%  65-122 CNYRGVRQRTWGK 667 72%  (72/118) WVAEIREPNRGSRL (42/58) WLGTFPTAISAALA YDEAARAMYGSCA RLNF 212 Gm/Glymal2g32400.1 60%  63-120 CNYRGVRQRTWGK 669 72%  (75/123) WVAEIREPNRGNRL (42/58) WLGTFPTAIGAALA YDEAARAMYGSCA RLNF 210 Gm/Glyma12g11150.1 60%  65-122 CNYRGVRQRTWGK 668 72%  (72/119) WVAEIREPNRGSRL (42/58) WLGTFPTAISAALA YDEAAMAMYGFCA RLNF 206 Eg/Eucgr.G03094.1 61%  69-126 FNYRGVRQRTWGK 666 70%  (74/121) WVAEIREPNRGSRL (41/58) WLGTFPTAIEAAKA YDEAATAMYGPCA RLNF 198 Si/Si002067m 60% 167-224 CPYRGVRQRTWGK 662 70%  (72/120) WVAEIREPNRGKRL (41/58) WLGSFPTAVEAAHA YDEAAKAMYGPKA RVNF 194 Bd/Bradi2g04000.1 56%  76-133 CAYRGVRQRTWGK 660 68%  (67/119) WVAEIREPNRGKRL (40/58) WLGSFPTAVEAAHA YDEAARAMYGAKA RVNF 196 Os/LOC_Os01g07120.1 55%  81-138 CAYRGVRQRTWGK 661 68%  (66/119) WVAEIREPNRGRRL (40/58) WLGSFPTALEAAHA YDEAARAMYGPTA RVNF 202 Si/Si022619m 58%  83-140 CGYRGVRQRTWGK 664 65%  (73/125) WVAEIREPNRANRL (38/58) WLGTFPTAEDAARA YDQAARAMYGEVA RTNF 204 Si/Si022621m 58%  82-139 CGYRGVRQRTWGK 665 65%  (73/125) WVAEIREPNRANRL (38/58) WLGTFPTAEDAARA YDQAARAMYGEVA RTNF 200 Bd/Bradi2g29960.1 56% 130-187 CKFRGVRQRTWGK 663 65%  (70/123) WVAEIREPNRVSRL (38/58) WLGTFPTAETAACA YDEAARAMYGPLA RTNF 220 Gm/Glyma07g19220.1 57%  65-129 CKFRGVRQRIWGK 673 63%  (73/128) WVAEIREPINGKLV (41/65) GEKANRLWLGTFST ALEAALAYDEAAKA MYGPCARLNF 222 Gm/Glyma18g43750.1 57%  65-129 CKFRGVRQRIWGK 674 63%  (73/127) WVAEIREPINGKLV (41/65) GEKANRLWLGTFST ALEAALAYDEAAKA LYGPCARLNF

These functionally-related and/or closely-related DREB2H clade polypeptides may be identified by a consensus AP2 domain sequence, SEQ ID NO: 852:

X¹X²X³GVRQRX⁹WGKWVX¹⁵EIREPX²¹X²²X²³X²⁴X²⁵X²⁶X²⁷X²⁸X²⁹X³⁰X³¹X³²LWLGX³⁷FX³⁹X⁴⁰X⁴¹X⁴²X⁴³AAX⁴⁶AYDX⁵⁰AX⁵²X⁵³AX⁵⁵YGX⁵⁸X⁵⁹ARX⁶²NX⁶⁴

where X¹=any amino acid; X²=F or Y; X³=any amino acid; X⁹=any amino acid; X¹⁵=A or G; X²¹=I or absent; X²²=N or absent; X²³=G or absent; X²⁴=K or absent; X²⁵=L or absent; X²⁶=V or absent; X²⁷=G or absent; X²⁸=any amino acid; X²⁹=any amino acid; X³⁰=any amino acid; X³¹=any amino acid; X³²=R or K; X³⁷=S or T; X³⁹=any amino acid; X⁴⁰=S or T; X⁴¹=A or S; X⁴²=any amino acid; X⁴³=any amino acid; X⁴⁶=any amino acid; X⁵⁰=Q, D, N or E; X⁵²=A or S; X⁵³=any amino acid; X⁵⁵=I, L, V or M; X⁵⁸=any amino acid; X⁵⁹=any amino acid; X⁶²=any amino acid; and X⁶⁴=F, I, L, V or M ERF087 Clade Polypeptides

TABLE 13 Conserved ‘AP2 domain’ of ERF087 and closely related sequences Col. 7 Percent identity of Col. 3 AP2 Percent Col. 4 Col. 6 domain in Col. 1 identity of AP2 SEQ ID Col. 5 to SEQ polypeptide domain in NO: of AP2 ID Col. 2 in Col. 1 to amino acid Col. 5 AP2 domain of NO: Species/Identifier ERF087 coordinates Conserved AP2 domain domain ERF087 246 At/ERF087 or 100%   38-101 KYVGVRRRPWGRY 686 100%  AT1G28160.1 (245/245) AAEIRNPTTKERYW (64/64) LGTFDTAEEAALAY DRAARSIRGLTART NFVYSDMPR 254 At/AT5G13910.1 83% 19-82 RFLGVRRRPWGRYA 690 85% (64/77) AEIRDPTTKERHWL (55/64) GTFDTAEEAALAYD RAARSMRGTRARTN FVYSDMPP 248 Eg/Eucgr.B03565.1 47%  46-109 RFLGVRRRPWGRYA 687 85% (104/221) AEIRDPTTKERHWL (55/64) GTFDTAEEAALAYD RAARSMRGAKART NFVYSDMPP 266 Vv/GSVIVT01032961001 84% 21-84 RFLGVRRRPWGRYA 696 84% (65/77) AEIRDPSTKERHWL (54/64) GTFDTAEEAALAYD RAARSMRGSRARTN FVYSDMPP 256 Pt/POPTR_0001s15710.1 81% 25-88 RFLGVRRRPWGRYA 691 84% (64/79) AEIRDPSTKERHWL (54/64) GTFDTAEEAALAYD RAARSMRGSRARTN FVYSDMPA 258 Pt/POPTR_0003s07540.1 81% 25-88 RFLGVRRRPWGRYA 692 84% (64/79) AEIRDPSTKERHWL (54/64) GTFDTAEEAALAYD RAARSMRGPRARTN FVYSDMPA 252 Pt/POPTR_0003s15940.1 70%  39-102 RFLGVRRRPWGRYA 689 84%  (84/120) AEIRDPSTKERHWL (54/64) GTFDTAEEAALAYD RAARSMRGSKARTN FVYSDMPP 250 Pt/POPTR_0001s12820.1 45%  37-100 RFLGVRRRPWGRYA 688 84% (109/240) AEIRDPSTKERHWL (54/64) GTFDTAEEAALAYD RAARSMRGSKARTN FVYSDMPP 262 Gm/Glyma02g07460.1 72% 31-94 RYLGVRRRPWGRY 694 82% (69/95) AAEIRDPSTKERHW (53/64) LGTFDTAEEAALAY DRAARSMRGSRART NFVYPDTPP 260 Eg/Eucgr.I01576.1 51% 27-90 RFLGVRRRPWGRYA 693 82%  (81/157) AEIRDPSTKERHWL (53/64) GTFDTAEEAALAYD RAARSMRGSRARTN FVYSDLPA 238 Os/LOC_Os02g32040.1 75%  39-102 RYLGVRRRPWGRY 682 79% (60/79) AAEIRDPATKERHW (51/64) LGTFDTAEEAAVAY DRAARTIRGAAART NFAYPDLPP 264 Gm/Glyma16g26460.1 70% 31-94 RYLGVRRRPWGRY 695 79% (67/95) AAEIRDPSTKERHW (51/64) LGTFDTAEEAALAY DKAARSMRGSRART NFIYPDTPP 240 Os/LOC_Os04g32790.1 69%  51-114 RYLGVRRRPWGRY 683 79% (62/89) AAEIRDPATKERHW (51/64) LGTFDTAEEAAVAY DRAARSLRGARART NFAYPDLPP 242 Zm/GRMZM2G023708_T01 69%  41-104 RYLGVRRRPWGRY 684 79% (62/89) AAEIRDPATKERHW (51/64) LGTFDTAEEAAVAY DRAARSLRGARART NFAYPDLPP 236 Zm/GRMZM2G047999_T01 64%  73-136 RYLGVRRRPWGRY 681 79%  (73/114) AAEIRDPATKERHW (51/64) LGTFDTAEEAAIAY DRAARNIRGANART NFAYPDLPP 244 Zm/GRMZM2G079825_T01 63%  37-100 RYLGVRRRPWGRY 685 79%  (73/115) AAEIRDPATKERHW (51/64) LGTFDTAEEAAVAY DRAARSLRGARART NFAYPDLPP 268 Gm/Glyma16g05070.1 49% 14-77 RYLGVRRRPWGRY 697 78%  (74/150) AAEIRDPSTKERHW (50/64) LGTFDTADEAALAY DRAARAMRGSRAR TNFVYADTTP

These functionally-related and/or closely-related ERF087 clade polypeptides may be identified by a consensus AP2 domain sequence, SEQ ID NO: 853:

X¹X²X³GVRRRPWGRYAAEIRX¹⁹PX²¹TKERX²⁶WLGTFDTAX³⁵EAAX³⁹AYDX⁴³AARX⁴⁷X⁴⁸RGX⁵¹X⁵²ARTNFX⁵⁸YX⁶⁰DX⁶²X⁶³X⁶⁴

where X¹=K or R; X²=F or Y; X³=I, L, V or M; X¹⁹=N or D; X²¹=A, S or T; X²⁶=H or Y; X³⁵=D or E; X³⁹=I, L, V or M; X⁴³=R or K; X⁴⁷=any amino acid; X⁴⁸=I, L, V or M; X⁵¹=any amino acid; X⁵²=any amino acid; X⁵⁸=any amino acid; X⁶⁰=S, A or P; X⁶²=any amino acid; X⁶³=T or P; and X⁶⁴=any amino acid. BBX18 Clade Polypeptides

TABLE 14 Conserved first ‘BBX domain’ of BBX18 and closely related sequences Col. 7 Percent identity of Col. 3 Col. 4 first BBX Percent BBX Col. 6 domain in Col. 1 identity of domain 1 SEQ ID Col. 5 to SEQ polypeptide in amino Col. 5 NO: of first BBX ID Col. 2 in Col. 1 to acid Conserved BBX BBX domain of NO: Species/Identifier BBX18 coordinates domain 1 domain 1 BBX18 278 At/BBX18 or 100%  5-42 CDACESAAAIVFCA 702 100%  AT2G21320.1 (172/172) ADEAALCCSCDEKV (38/38) HKCNKLASRH 290 Pt/POPTR_0007s13830.1 61% 5-42 CDACESAAAIVFCA 708 92% (114/184) ADEAALCLACDEKV (35/38) HMCNKLASRH 284 Gm/Glyma01g37370.1 60% 5-42 CDACESAAAIVFCA 705 92% (111/183) ADEAALCRACDEKV (35/38) HMCNKLASRH 286 Gm/Glyma11g07930.1 59% 5-42 CDACESAAAIVFCA 706 92% (112/189) ADEAALCRACDEKV (35/38) HMCNKLASRH 296 Pt/POPTR_0004s16950.1 60% 5-42 CDVCESAAAILFCA 711 89% (111/184) ADEAALCRSCDEKV (34/38) HMCNKLASRH 298 Pt/POPTR_0009s12730.1 60% 5-42 CDVCESAAAILFCA 712 89% (111/184) ADEAALCRSCDEKV (34/38) HLCNKLASRH 300 Vv/GSVIVT01024173001 59% 5-42 CDACESAAAILFCA 713 89% (117/198) ADEAALCRACDEKV (34/38) HMCNKLASRH 302 Sl/Solyc01g110370.2.1 58% 5-42 CDVCESAAAILFCA 714 89% (114/196) ADEAALCRSCDEKV (34/38) HLCNKLASRH 280 At/AT4G38960.1 76% 5-42 CDACENAAAIIFCAA 703 86% (131/171) DEAALCRPCDEKVH (33/38) MCNKLASRH 288 Pt/POPTR_0005s11900.1 61% 5-42 CDACESAFAIVFCAA 707 86% (114/184) DEAALCLACDKKVH (33/38) MCNKLASRH 292 Vv/GSVIVT01018818001 60% 5-42 CDVCESAAAILFCA 709 86% (110/183) ADEAALCRVCDEKV (33/38) HMCNKLASRH 282 Eg/Eucgr.I02368.1 57% 5-42 CDACESAAAVVFCA 704 86% (107/185) ADEAALCSACDDKV (33/38) HMCNKLASRH 306 Gm/Glyma12g04130.1 63% 5-42 CDVCESAAAIVFCA 716 84% (110/172) ADEAALCSACDHKI (32/38) HMCNKLASRH 294 Eg/Eucgr.I01328.1 57% 5-42 CDVCENAAAIFFCA 710 84% (111/193) ADEAALCRACDEKV (32/38) HLCNKLASRH 270 Bd/Bradi4g35950.1 55% 5-42 CDVCESAVAVLFCA 698 84% (108/196) ADEAALCRSCDEKV (32/38) HLCNKLASRH 274 Zm/GRMZM2G143718_T01 57% 5-42 CDVCESAPAVLFCA 700 81% (109/191) ADEAALCRPCDEKV (31/38) HMCNKLASRH 276 Zm/GRMZM2G422644_T01 57% 5-42 CDVCESAPAVLFCA 701 81% (109/190) ADEAALCRPCDEKV (31/38) HMCNKLASRH 304 Gm/Glyma11g11850.1 57% 5-42 CDVCESAAAILFCA 715 81% (112/196) ADEAALC S ACDHKI (31/38) HMCNKLASRH 272 Os/LOC_Os09g35880.1 57% 5-42 CDVCESAPAVLFCV 699 78% (113/197) ADEAALC RSCDEKV (30/38) HMCNKLARRH

TABLE 15 Conserved second ‘BBX domain’ of BBX18 and closely related sequences Col. 7 Percent identity of second BBX Col. 3 Col. 4 domain in Percent BBX Col. 6 Col. 5 to Col. 1 identity of domain 2 SEQ ID second SEQ polypeptide in amino Col. 5 NO: of BBX ID Col. 2 in Col. 1 to acid Conserved BBX BBX domain of NO: Species/Identifier BBX18 coordinates domain 2 domain 2 BBX18 278 At/BBX18 or 100%  56-91 CDICENAPAFFYCEI 721 100%  AT2G21320.1 (172/172) DGSSLCLQCDMVVH (36/36) VGGKRTH 280 At/AT4G38960.1 76% 56-91 CDICENAPAFFYCEI 722 100% (131/171) DGSSLCLQCDMVVH (36/36) VGGKRTH 306 Gm/Glyma12g04130.1 63% 56-91 CDICENAPAFFYCEI 735 97% (110/172) DGSSLCLQCDMIVH (35/36) VGGKRTH 298 Pt/POPTR_0009s12730.1 60% 56-91 CDICENAPAFFYCEI 731 97% (111/184) DGSSLCLQCDMIVH (35/36) VGGKRTH 302 Sl/Solyc01g110370.2.1 58% 56-91 CDICENAPAFFYCEI 733 97% (114/196) DGSSLCLQCDMIVH (35/36) VGGKRTH 294 Eg/Eucgr.I01328.1 57% 56-91 CDICENAPAFFYCEI 729 97% (111/193) DGSSLCLQCDMLVH (35/36) VGGKRTH 304 Gm/Glyma11g11850.1 57% 56-91 CDICENAPAFFYCEI 734 97% (112/196) DGSSLCLQCDMIVH (35/36) VGGKRTH 288 Pt/POPTR_0005s11900.1 61% 56-91 CDICENAPAFFYCET 726 94% (114/184) DGSSLCLQCDMTVH (34/36) VGGKRTH 290 Pt/POPTR_0007s13830.1 61% 56-91 CDICENAPAFFYCET 727 94% (114/184) DGSSLCLQCDMTVH (34/36) VGGKRTH 296 Pt/POPTR_0004s16950.1 60% 56-91 CDICEKAPAFFYCEI 730 94% (111/184) DGSSLCLQCDMIVH (34/36) VGGKRTH 284 Gm/Glyma01g37370.1 60% 56-91 CDICENAPAFFYCET 724 94% (111/183) DGSSLCLQCDMIVH (34/36) VGGKRTH 292 Vv/GSVIVT01018818001 60% 56-91 CDICENAPAFFYCEI 728 94% (110/183) DGTSLCLQCDMIVH (34/36) VGGKRTH 286 Gm/Glyma11g07930.1 59% 56-91 CDICENAPAFFYCET 725 94% (112/189) DGSSLCLQCDMIVH (34/36) VGGKRTH 300 Vv/GSVIVT01024173001 59% 56-91 CDICENAPAFFYCEV 732 91% (117/198) DGTSLCLQCDMIVH (33/36) VGGKRTH 272 Os/LOC_Os09g35880.1 57% 56-91 CDICENAPAFFYCEI 718 91% (113/197) DGTSLCLSCDMTVH (33/36) VGGKRTH 282 Eg/Eucgr.I02368.1 57% 56-91 CDICENAPAFFYCEV 723 91% (107/185) DGTSLCLQCDMIVH (33/36) VGGKRTH 274 Zm/GRMZM2G143718_T01 57% 56-91 CDICENSPAFFYCEI 719 88% (109/191) DGTSLCLSCDMTVH (32/36) VGGKRTH 276 Zm/GRMZM2G422644_T01 57% 56-91 CDICENSPAFFYCEI 720 88% (109/190) DGTSLCLSCDMTVH (32/36) VGGKRTH 270 Bd/Bradi4g35950.1 55% 56-91 CDICENSPAFFYCDI 717 86% (108/196) DGTSLCLSCDMAVH (31/36) VGGKRTH

These functionally-related and/or closely-related BBX18 clade polypeptides may be identified by a first consensus BBX domain sequence (BBX1), SEQ ID NO: 854:

CDX³CEX⁶AX⁸AX¹⁰X¹¹FCX¹⁴ADEAALCX²²X²³CDX²⁶KX²⁸HX³⁰CNKLAX³⁶RH

where X³=any amino acid; X⁶=any amino acid; X⁸=any amino acid; X¹⁰=I, L, V or M; X¹¹=F, I, L, V or M; X¹⁴=any amino acid; X²²=any amino acid; X²³=any amino acid; X²⁶=any amino acid; X²⁸=I, L, V or M; X³⁰=any amino acid; and X³⁶=any amino acid.

These functionally-related and/or closely-related BBX18 clade polypeptides may also be identified by a second consensus BBX domain sequence (BBX2), SEQ ID NO: 855:

CDICEX⁶X⁷PAFFYCX¹⁴X¹⁵DGX¹⁸SLCLX²³CDMX²⁷VHVGGKRTH

X⁶=N or K; X⁷=S or A; X¹⁴=D or E; X¹⁵=T, I, L, V or M; X¹⁸=S or T; X²³=I, L, V or M; and X²⁷=I, L, V or M.

bHLH60 Clade Polypeptides

TABLE 16 Conserved ‘bHLH domain’ of bHLH60 and closely related sequences Col. 7 Percent identity of Col. 3 bHLH Percent Col. 4 Col. 6 domain in Col. 1 identity of bHLH SEQ ID Col. 5 to SEQ polypeptide domain in Col. 5 NO: of bHLH ID Col. 2 in Col. 1 to amino acid Conserved bHLH bHLH domain of NO: Species/Identifier bHLH60 coordinates domain domain bHLH60 318 At/bHLH60 or 100%  208-265 RGQATDSHSLAER 741 100%  AT3G57800.2 (379/379) ARREKINARMKLL (58/58) QELVPGCDKIQGTA LVLDEIINHVQSLQ RQVE 316 At/AT2G42300.1 68% 189-246 RGQATDNHSLAER 740 96% (261/380) ARREKINARMKLL (56/58) QELVPGCDKIQGTA LVLDEIINHVQTLQ RQVE 330 Cc/clementine0.9_015567m 55% 242-299 RGQATDSHSLAER 747 96% (178/321) ARREKINARMKLL (56/58) QELVPGCNKISGTA LVLDEIINHVQSLQ RQVE 322 Gm/Glyma03g29710.1 53% 210-267 RGQATDSHSLAER 743 96% (190/352) ARREKINARMKLL (56/58) QELVPGCDKISGTA MVLDEIINHVQSLQ RQVE 324 Gm/Glyma19g32570.1 52% 204-261 RGQATDSHSLAER 744 96% (203/388) ARREKINARMKLL (56/58) QELVPGCDKISGTA MVLDEIINHVQSLQ RQVE 328 Cc/clementine0.9_011877m 51% 242-299 RGQATDSHSLAER 746 96% (214/418) ARREKINARMKLL (56/58) QELVPGCNKISGTA LVLDEIINHVQSLQ RQVE 334 Vv/GSVIVT01033350001 55% 201-258 RGQATDSHSLAER 749 94% (218/396) ARREKINARMKLL (55/58) QELVPGCNKISGTA LVLDEIISHVQSLQR QVE 320 Eg/Eucgr.A02413.1 52% 185-242 RGQATDSHSLAER 742 94% (179/338) ARREKINARMKLL (55/58) QELVPGC S KIS GTA SVLDEIINHVQSLQ RQVE 336 Sl/Solyc10g079070.1.1 47% 198-255 RGQATDSHSLAER 750 94% (163/342) ARREKINARMKLL (55/58) QELVPGCNKISGTA MVLDEIINHVQSLQ RQVE 332 Pt/POPTR_0006s05600.1 53% 181-238 RGQATDSHSLAER 748 93% (188/354) ARREKINQRMKLL (54/58) QELVPGCNKISGTA LVLDEIINHVQSLQ CQVE 326 Gm/Glyma10g12210.1 46% 196-253 RGQATDSHSLAER 745 91% (179/386) ARREKINARMKLL (53/58) QELVPGCNKISGTA LVLDKIINHVQSLQ NEVE 310 Zm/GRMZM2G074438_T01 43% 161-218 RGQATDSHSLAER 737 91% (134/309) ARREKINARMELL (53/58) KELVPGCSKVSGTA LVLDEIINHVQSLQ RQVE 314 Si/Si006781m 43% 177-234 RGQATDSHSLAER 739 91% (132/307) ARREKINARMELL (53/58) KELVPGCSKVSGTA LVLDEIINHVQSLQ RQVE 312 Zm/GRMZM2G378653_T01 43% 184-241 RGQATDSHSLAER 738 91% (135/309) ARREKINARMELL (53/58) KELVPGCSKVSGTA LVLDEIINHVQSLQ RQVE 308 Bd/Bradi1g35990.1 42% 145-202 RGQATDSHSLAER 736 91% (147/348) ARREKINARMELL (53/58) KELVPGCSKVSGTA LVLDEIINHVQSLQ RQVE

These functionally-related and/or closely-related bHLH60 clade polypeptides may be identified by a consensus bHLH domain sequence, SEQ ID NO: 856:

RGQATDX⁷HSLAERARREKINX²¹RMX²⁴LLX²⁷ELVPGCX³⁴KX³⁶X³⁷GTAX⁴¹VLDX⁴⁵II⁴⁸HVQX⁵²LQX⁵⁵X⁵⁶VE

where X⁷=any amino acid; X²¹=any amino acid; X²⁴=K or E; X²⁷=Q or K; X³⁴=any amino acid; X³⁶=I, L, V or M; X³⁷=any amino acid; X⁴¹=any amino acid; X⁴⁵=K or E; X⁴⁸=any amino acid; X⁵²=S or T; X⁵⁵=any amino acid; and X⁵⁶=Q or E.

NF-YC6 Clade Polypeptides

TABLE 17 Conserved ‘NF-Y/histone-like domain’ of NF-YC6 and closely related sequences Col. 7 Percent identity of NF- Y/histone- like Col. 4 Col. 6 domain in Col. 3 NF- SEQ ID Col. 5 to Percent Y/histone- NO: of NF- Col. 1 identity of like domain NF- Y/histone- SEQ polypeptide in amino Col. 5 Y/histone- like ID Col. 2 in Col. 1 to acid Conserved NF- like domain of NO: Species/Identifier NF-YC6 coordinates Y/histone-like domain domain NF-YC6 356 At/NF-YC6 or 100%   53-117 RQLPLARIKKIMKA 760 100%  AT5G50480.1 (202/202) DPDVHMVSAEAPII (65/65) FAKACEMFIVDLT MRSWLKAEENKRH TLQKSDISNAV 348 Si/Si015775m 55%  55-119 HSLPLARIKKIMKA 756 67% (57/103) DEDVKMIAAEAPV (44/65) VFAKACEMFILELT LRSWLHTEGTKRR TMQRSDVSAAI 350 At/AT5G27910.1 54% 35-99 HDLPITRIKKIMKY 757 67% (92/168) DPDVTMIASEAPIL (44/65) LSKACEMFIMDLT MRSWLHAQESKRV TLQKSNVDAAV 338 Bd/Bradi3g17790.1 52%  77-141 HSLPLARIKKIMKA 751 67% (55/105) DEDVQMIAGEAPA (44/65) VFAKACEMFILELT LRSWLQTRENNRN TLQKNDIATVV 346 Os/LOC_Os08g10560.1 47% 380-444 PNLPLARIKKIMKA 755 63% (59/125) DEDVKMIAGEAPA (41/65) LFAKACEMFILDMT LRSWQHFLEGRRR TLQRSDVEAVI 340 Bd/Bradi3g17800.1 48% 240-305 HSLPLARIKKIMKA 752 60% (56/116) SGENVQMIAGEAH (40/66) GLLAKACEIFIQELT LRSWLQTRENNRR TLQKNDIAAAV 344 Bd/Bradi3g17810.1 51%  99-164 HSLPLARIKKIMKA 754 59% (51/100) SGEDIRMIASEAPG (39/66) LLAKASEIFIQELTL RSWLETRDNNRRT LQKNDIGAAV 352 At/AT5G50490.1 45% 35-99 HEFPISRIKRIMKED 758 58% (78/172) PDVSMIAAEAPNLL (38/65) SKACEMFVMDLTM RSWLHAQESNRLTI RKSDVDAVV 368 Sl/Solyc03g111460.1.1 43%  64-128 HSLPISRIKKIMKSD 766 58% (69/158) KEVRMISAESPILLA (38/65) KACELFIQELTHRS WLKAQECQRQTLK KIDLFTVL 342 Bd/Bradi3g17820.1 52%  7-72 HSLPLERIKKIMKA 753 56% (45/85)  SGENVQVIAGEAPG (37/66) VLTKACEIFIQELTL RSWLQTREKNRRT LQKNDIAAAV 370 Sl/Solyc03g111470.1.1 48%  74-138 HSLPIFRIKKIMKSD 767 56% (45/92)  KEVRMISAESPILLD (37/65) KACELFIQELTHRS WLKAQECQRRTLK KIDFFTTE 354 At/AT5G50470.1 48%  62-132 HAFPLTRIKKIMKS 759 56% (92/189) NPEVNMVTAEAPV (40/71) LISKACEMLILDLT MRSWLHTVEGGRQ TLKRSDTLTRSDIS AAT 362 Sl/Solyc03g110840.1.1 49%  52-117 RLLLPPTRIKKIMK 763 53% (51/104) KNEDVRMVAGESP (35/66) VLLAKACELFIQDL TLRSSIHAQENHRRI LKKDDLTDVI 364 Sl/Solyc03g110850.1.1 46%  53-118 NLLPRIHRIKKIMKT 764 53% (54/116) DKDVRMIATESPVL (35/66) LAKACELFIQELTL RSWFKAEENHRRIL KKDDVTDVI 366 Sl/Solyc11g016920.1.1 45%  53-118 NLLPSINRIKKIMKT 765 50% (53/116) DKDVRMIATESPVL (33/66) LAKACELFIQELTL RSWFKTEKNHRRIL KKDDVTDVI 360 Sl/Solyc02g021330.1.1 40%  54-119 NHLLPPNLIKKLMK 762 46% (55/137) TDEDDQMIAAESPV (31/66) LLAKTCELFIQELTL RSWLNAQEKHQHI LKKDDVTDVI 358 Sl/Solyc00g107050.1.1 42%  55-120 NLLVSPNRIKNIMK 761 45% (40/94)  TNKDVRRITSESPV (30/66) LLAKACDFFIQELT LRSWLNAQENHRR ILKKKDVTDVI 372 Sl/Solyc03g111450.1.1 40% 102-166 HHFPISRIKRIIKSEN 768 44% (69/171) NAIKLSAETPILFSK (29/65) ACELFVLELTLRSW FHAQQNNRGSLKK TDFAAAI

These functionally-related and/or closely-related NF-YC6 clade polypeptides may be identified by a consensus NF-Y/histone-like domain sequence, SEQ ID NO: 857:

X¹X²X³X⁴X⁵X⁶X⁷X⁸IKX¹¹X¹²X¹³KX¹⁵X¹⁶X¹⁷X¹⁸X¹⁹X²⁰X²¹X²²X²³X²⁴X²⁵EX²⁷X²⁸X²⁹X³⁰X³¹X³²KX³⁴X³⁵X³⁶X³⁷X³⁸X³⁹X⁴⁰X⁴¹X⁴²TX⁴⁴RsX⁴⁷X⁴⁸X⁴⁹X⁵⁰X⁵¹X⁵²X⁵³X⁵⁴X⁵⁵X⁵⁶X⁵⁷X⁵⁸X⁵⁹X⁶⁰X⁶¹X⁶²X⁶³X⁶⁴X⁶⁵X⁶⁶X⁶⁷X⁶⁸X⁶⁹X⁷⁰X⁷¹X⁷²X⁷³

where X¹=any amino acid; X²=any amino acid; X³=F, I, L, V or M; X⁴=any amino acid or absent; X⁵=any amino acid; X⁶=any amino acid; X⁷=any amino acid; X⁸=any amino acid; X¹¹=N, K or R; X¹²=I, L, V or M; X¹³=I, L, V or M; X¹⁵=any amino acid; X¹⁶=any amino acid; X¹⁷=G or absent; X¹⁸=any amino acid; X¹⁹=N, E or D; X²⁰=any amino acid; X²¹=any amino acid; X²²=any amino acid; X²³=I, L, V or M; X²⁴=S, A or T; X²⁵=A, S, T or G; X²⁷=A, S or T; X²⁸=any amino acid; X²⁹=any amino acid; X³⁰=I, L, V or M; X³¹=F, I, L, V or M; X³²=any amino acid; X³⁴=any amino acid; X³⁵=S or C; X³⁶=E or D; X³⁷=F, I, L, V or M; X³⁸=I, L, V or M; X³⁹=I, L, V or M; X⁴⁰=any amino acid; X⁴¹=E or D; X⁴²=I, L, V or M; X⁴⁴=any amino acid; X⁴⁷=any amino acid; X⁴⁸=any amino acid; X⁴⁹=any amino acid; X⁵⁰=A or T; X⁵¹=any amino acid; X⁵²=any amino acid; X⁵³=any amino acid; X⁵⁴=any amino acid; X⁵⁵=Q, R; X⁵⁶=any amino acid; X⁵⁷=any amino acid; X⁵⁸=I, L, V or M; X⁵⁹=K, Q, R; X⁶⁰=R or absent; X⁶¹=S or absent; X⁶²=D or absent; X⁶³=T or absent; X⁶⁴=L or absent; X⁶⁵=T or absent; X⁶⁶=K, R; X⁶⁷=any amino acid; X⁶⁸=N, D; X⁶⁹=F, I, L, V or M; X⁷⁰=any amino acid; X⁷¹=any amino acid; X⁷²=A, T, V; and X⁷³=any amino acid. bHLH121 Clade Polypeptides

TABLE 18 Conserved ‘bHLH domain’ of bHLH121 and closely related sequences Col. 7 Percent identity of Col. 3 bHLH Percent Col. 4 Col. 6 domain in Col. 1 identity of bHLH SEQ ID Col. 5 to SEQ polypeptide domain in Col. 5 NO: of bHLH ID Col. 2 in Col. 1 to amino acid Conserved bHLH bHLH domain of NO: Species/Identifier bHLH121 coordinates domain domain bHLH121 388 At/bHLH121 100%   6-60 RKSQKAGREKLRR 813 100%  or (284/284) EKLNEHFVELGNV (55/55) AT3G19860.1 LDPERPKNDKATIL TDTVQLLKELTSEV N 390 Cc/clementine0.9_014901m 64%  60-114 RKMQKADREKLRR 814 80% (185/288) DRLNEHFFELGNAL (44/55) DPDRPKNDKATILA DTVQLLKDLTSQV E 392 Cc/clementine0.9_014926m 64%  60-114 RKMQKADREKLRR 815 80% (185/288) DRLNEHFFELGNAL (44/55) DPDRPKNDKATILA DTVQLLKDLTSQV E 400 Pt/POPTR_0004s17540.1 62% 42-96 RKIQKADREKLRR 819 80% (156/249) DRLNEHFVELGNTL (44/55) DPDRPKNDKATILA DTIQLLKDLTSQVD 402 Pt/POPTR_0009s13220.1 61% 38-92 RKIQKADREKLRR 820 80% (176/288) DRLNEHFVELGNTL (44/55) DPDRPKNDKATILA DTVQLLKDLNSKV D 386 Vv/GSVIVT01018777001 56%  50-104 RKVQKADREKLRR 812 78% (141/248) DRLNEHFLELGNTL (43/55) DPDRPKNDKATILA DTIQMLKDLTAEV N 382 Gm/Glyma07g26910.1 53%  56-110 RKVLKADREKLRR 810 78% (123/232) DRLNEHFQELGNA (43/55) LDPDRPKNDKATIL TETVQMLKDLTAE VN 394 Gm/Glyma08g15740.1 65%  7-61 RKTQKADREKLRR 816 76% (157/238) DRLNEQFVELGNIL (42/55) DPDRPKNDKATIIG DTIQLLKDLTSQVS 398 Gm/Glyma12g02740.1 57%  7-61 RKTQKADREKLRR 818 76% (137/239) DRFNVQFVELGNIL (42/55) DPDRPKNDKATILG DTIQLLKDLTSEVS 396 Gm/Glyma15g29630.1 63% 21-75 RKTQKADREKLRR 817 74% (151/238) DRINEQFVELGNIL (41/55) DPDRPKNDKATILC DTIQLLKDLISQVS 404 Vv/GSVIVT01024084001 57%  46-100 RKVQKADREKLRR 821 74% (166/288) DRLNEQFIELGNAL (41/55) DPDRPKNDKATILS DTIQLLKDLTAQVE 384 Pt/POPTR_0005s11550.1 51%  61-115 KKVQKADREKLRR 811 74% (116/227) DNLNEQFLELGTTL (41/55) DPDRPKNDKATILT DTIQVLKDLTAEVN 378 Si/Si017804m 48% 36-90 RKVQKADREKMRR 808 74% (130/268) DKLNEQFQELGNT (41/55) LDPDRPRNDKATIL GDTIQMLKDLTSH VN 406 St/Solyc11g111130.2.1 61%  57-111 RKVQKADREKLRR 822 70% (151/247) DRLNEQFMELGKT (39/55) LDPDRPKNDKASIL SDTVQILKDLTAQV S 408 Zm/GRMZM2G114444_T02 50% 30-84 RKVQKADREKMRR 823 70% (119/236) DKLNEQFQDLGNA (39/55) LDPDRPRNDKATIL GDTIQMLKDLTTQ VN 374 Bd/Bradi3g11520.1 49% 40-94 RKVQKADRERMRR 806 69% (127/256) DKLNEQFQELGTTL (38/55) DPDRPRNDKATILG DTIQMLKDLSSQVN 376 Os/LOC_Os02g23823.1 48% 40-94 RKVQKADREKMRR 807 69% (116/241) DRLNEQFQELGSTL (38/55) DPDRPRNDKATILS DAIQMLKDLTSQV N 380 At/AT4G36060.1 65% 41-99 KKEAVCSQKAERE 809 61%  (68/104) KLRRDKLKEQFLEL (36/59) GNALDPNRPKSDK ASVLTDTIQMLKD VMNQVD

TABLE 19 Conserved ‘putative leucine zipper domain’ of bHLH121 and closely related sequences Col. 7 Percent identity of putative leucine zipper Col. 4 Col. 6 domain in Col. 3 Putative SEQ ID Col. 5 to Percent leucine NO: of putative Col. 1 identity of zipper putative leucine SEQ polypeptide domain in Col. 5 leucine zipper ID Col. 2 in Col. 1 to amino acid Conserved putative zipper domain of NO: Species/Identifier bHLH121 coordinates leucine zipper domain domain bHLH121 388 At/bHLH121 100%  61-97 KLKSEYTALTDESR 831 100%  or (284/284) ELTQEKNDLREEKT (37/37) AT3G19860.1 SLKSDIENL 406 Sl/Solyc01g111130.2.1 61% 112-148 RLKSEYAALTDESR 840 89% (151/247) ELTQEKNDLREEK (33/37) ASLKSDIESL 394 Gm/Glyma08g15740.1 65% 62-98 KLKDEYATLNEESR 834 81% (157/238) ELTQEKNDLREEK (30/37) ASLKSDIGNL 390 Cc/clementine0.9_014901m 64% 115-151 KLKTEHAALTEESR 832 81% (185/288) ELTQEKNDLREEKL (30/37) SLRSEIENL 392 Cc/clementine0.9_014926m 64% 115-151 KLKTEHAALTEESR 833 81% (185/288) ELTQEKNDLREEKL (30/37) SLRSEIENL 400 Pt/POPTR_0004s17540.1 62%  97-133 KLKAEYATLSEESL 837 81% (156/249) ELTQEKNDLREEK (30/37) ASLKSDIENL 402 Pt/POPTR_0009s13220.1 61%  93-129 KLKAEHAALSEESR 838 78% (176/288) ELTLEKNDLREEKA (29/37) SLKSDVENL 396 Gm/Glyma15g29630.1 63%  76-112 KLKDEYAMLNEES 835 75% (151/238) RELTLEKTDLREEK (28/37) ASLKSDIDNL 404 Vv/GSVIVT01024084001 57% 101-137 KLKAENASLNEESR 839 75% (166/288) ELTQEKNDLREEK (28/37) ASLKSATENL 382 Gm/Glyma07g26910.1 53% 111-147 RLKTEHKTLSEESR 828 75% (123/232) ELMQEKNELREEK (28/37) TSLKSDIENL 374 Bd/Bradi3g11520.1 49%  95-131 KLKAEYSSLSEEER 824 72% (127/256) ELTQEKNELRDEK (27/37) ASLKSDIDNL 398 Gm/Glyma12g02740.1 57%  62-98 KLKDEYATLNEESC 836 70% (137/239) ELAQEKNELREEK (26/37) ASLKSDILKL 386 Vv/GSVIVT01018777001 56% 105-141 RLKVECAALSEESR 830 70% (141/248) ELVQEKNELREEK (26/37) VALKSDIDNL 378 Si/Si017804m 48%  91-127 KLKAEYTSLSEEAR 826 70% (130/268) ELTQEKNELRDEK (26/37) ASLKSEVDNL 380 At/AT4G36060.1 65% 100-136 RLKAEYETLSQESR 827 67%  (68/104) ELIQEKSELREEKA (25/37) TLKSDIEIL 408 Zm/GRMZM2G114444_T02 50%  85-121 KLKAEYTSLSEEAC 841 67% (119/236) ELTQEKNELRDEK (25/37) ASLKSEVDNL 376 Os/LOC_Os02g23823.1 48%  95-131 KLKAEYTSLSEEAR 825 67% (116/241) ELTQEKNELRDEK (25/37) VSLKFEVDNL 384 Pt/POPTR_0005s11550.1 51% 116-152 RLKAECATLSEETH 829 62% (116/227) ELMQEKNELREEK (23/37) ASLKADTENL

These functionally-related and/or closely-related bHLH121 clade polypeptides may be identified by a consensus bHLH domain sequence, SEQ ID NO: 858:

X¹KX³X⁴X⁵X⁶X⁷X⁸KAX¹¹REX¹⁴X¹⁵RRX¹⁸X¹⁹X²⁰X²¹X²²X²³FX²⁵X²⁶LGX²⁹X³⁰LDPX³⁴RPX³⁷X³⁸DK AX⁴²X⁴³X⁴⁴X⁴⁵X⁴⁶X⁴⁷X⁴⁸QX⁵⁰LKX⁵³X⁵⁴X⁵⁵X⁵⁶X⁵⁷VX⁵⁹

where X¹=K or R; X³=E or absent; X⁴=A or absent; X⁵=V or absent; X⁶=C or absent; X⁷=any amino acid; X⁸=any amino acid; X¹¹=any amino acid; X¹⁴=K or R; X¹⁵=I, L, V or M; X¹⁸=D or E; X¹⁹=N, K or R; X²⁰=F, I, L, V or M; X²¹=N or K; X²²=any amino acid; X²³=H or Q; X²⁵=any amino acid; X²⁶=D or E; X²⁹=any amino acid; X³⁰=any amino acid; X³⁴=N, D or E; X³⁷=K or R; X³⁸=any amino acid; X⁴²=S or T; X⁴³=I, L, V or M; X⁴⁴=I, L, V or M; X⁴⁵=any amino acid; X⁴⁶=D, E; X⁴⁷=A or T; X⁴⁸=I, L, V or M; X⁵⁰=I, L, V or M; X⁵³=D or E; X⁵⁴=I, L, V or M; X⁵⁵=any amino acid; X⁵⁶=any amino acid; X⁵⁷=any amino acid; and X⁵⁹=any amino acid.

These functionally-related and/or closely-related bHLH121 clade polypeptides may also be identified by a consensus putative leucine zipper domain sequence, SEQ ID NO: 859:

X¹LKX⁴EX⁶X⁷X⁸LX¹⁰X¹¹EX¹³X¹⁴ELX¹⁷X¹⁸EKX²¹X²²LRX²⁵EKX²⁸X²⁹LX³¹X³²X³³X³⁴X³⁵X³⁶L

where X¹=R or K; X⁴=any amino acid; X⁶=any amino acid; X⁷=any amino acid; X⁸=any amino acid; X¹⁰=any amino acid; X¹¹=Q, D or E; X¹³=any amino acid; X¹⁴=any amino acid; X¹⁷=A, I, L, V or M; X¹⁸=any amino acid; X²¹=any amino acid; X²²=D or E; X²⁵=D or E; X²⁸=any amino acid; X²⁹=S, A or T; X³¹=K or R; X³²=any amino acid; X³³=any amino acid; X³⁴=T, I, L, V or M; X³⁵=any amino acid; and X³⁶=any amino acid. BBX26 Clade Polypeptides

TABLE 20 Conserved ‘BBX domain’ of BBX26 and closely related sequences Col. 7 Percent identity of Col. 3 BBX Percent Col. 4 Col. 6 domain in Col. 1 identity of BBX SEQ ID Col. 5 to SEQ polypeptide domain in Col. 5 NO: of BBX ID Col. 2 in Col. 1 to amino acid Conserved BBX BBX domain of NO: Species/Identifier BBX26 coordinates domain domain BBX26 410 At/BBX26 or 100%  5-41 CHTCRHVTAVIHC 769 100%  AT1G60250.1 (251/251) VTEALNFCLTCDNL (37/37) RHHNNIHAEH 412 At/AT1G68190.1 33% 14-51  CEFCKAYRAVVYCI 770 36% (28/84) ADTANLCLTCDAK (14/38) VHSANSLSGRH 414 Pt/POPTR_0008s12410.1 33% 5-42 CEFCMALRPVVYC 771 31% (24/71) NADAAYLCLSCDA (12/38) KVHSANALFNRH 420 Sl/Solyc04g007470.2 26% 7-44 CEFCMLLKPVVYC 774 31% (25/94) EADAAHLCLSCDA (12/38) KVHSANALSNRH 416 Gm/Glyma10g41540.1 27% 5-42 CEFCTALRPLVYCK 772 28% (22/79) ADAAYLCLSCDAK (11/38) VHLANAVSGRH 418 Gm/Glyma20g25700.1 27% 5-42 CEFCTALRPLVYCK 773 28% (22/79) ADAAYLCLSCDSK (11/38) VHLANAVSGRH

These functionally-related and/or closely-related BBX26 clade polypeptides may be identified by a consensus BBX domain sequence, SEQ ID NO: 860:

CX²X³CX⁵X⁶X⁷X⁸X⁹X¹⁰X¹¹X¹²CX¹⁴X¹⁵X¹⁶X¹⁷X¹⁸X¹⁹X²⁰CLX²³CDX²⁶X²⁷X²⁸HX³⁰X³¹NX³³X³⁴X³⁵X³⁶X³⁷H

where X²=any amino acid; X³=any amino acid; X⁵=any amino acid; X⁶=any amino acid; X⁷=Y, I, L, V, or M; X⁸=any amino acid; X⁹=A or P; X¹⁰=I, L, V, or M; X¹¹=I, L, V, or M; X¹²=any amino acid; X¹⁴=any amino acid; X¹⁵=A or T; X¹⁶=D or E; X¹⁷=A or T; X¹⁸=any amino acid; X¹⁹=any amino acid; X²⁰=F, I, L, V, or M; X²³=S or T; X²⁶=any amino acid; X²⁷=any amino acid; X²⁸=any amino acid; X³⁰=any amino acid; X³¹=A or absent; X³³=any amino acid; X³⁴=I, L, V, or M; X³⁵=any amino acid; X³⁶=any amino acid; and X³⁷=any amino acid. bHLH121 Clade Polypeptides

TABLE 21 Conserved ‘Methyltransferase domain’ of PMT24 and closely related sequences Col. 7 Percent identity of methyl- transferase Col. 3 Col. 6 domain in Percent Col. 4 SEQ ID Col. 5 to Col. 1 identity of Methyltransferase Col. 5 NO: of methyl- SEQ Col. 2 polypeptide domain in Conserved methyl- transferase ID Species/ in Col. 1 to amino acid methyltransferase transferase domain of NO: Identifier PMT24 coordinates domain domain PMT24 444 At/bHLH121 100%  367-584 VILDVGCGVASFGG 786 100%  or (770/770) YLFDRDVLALSFAP (218/218) AT1G29470.1 KDEHEAQVQFALE RGIPAMSNVMGTK RLPFPGSVFDLIHC ARCRVPWHIEGGK LLLELNRALRPGGF FVWSATPVYRKTE EDVGIWKAMSKLT KAMCWELMTIKKD ELNEVGAAIYQKP MSNKCYNERSQNE PPLCKDSDDQNAA WNVPLEACIHKVT EDSSKRGAVWPES WPERVETVPQWLD SQEGVY 446 At/AT2G34300.1 81% 367-584 VILDVGCGVASFGG 787 92% (638/783) YLFERDVLALSFAP (202/218) KDEHEAQVQFALE RGIPAMLNVMGTK RLPFPGSVFDLIHC ARCRVPWHIEGGK LLLELNRALRPGGF FVWSATPVYRKNE EDSGIWKAMSELT KAMCWKLVTIKKD KLNEVGAAIYQKPT SNKCYNKRPQNEPP LCKDSDDQNAAW NVPLEACMHKVTE DSSKRGAVWPNM WPERVETAPEWLD SQEGVY 450 Pt/POPTR_0005s20670.1 66% 423-640 VILDVGCGVASFGG 789 81% (548/826) YLFERDVLAMSFAP (177/218) KDEHEAQVQFALE RGIPAMLAVMGTK RLPFPSSVFDVVHC ARCRVPWHVEGGK LLLELNRVLRPGGY FVWSATPVYQKLP EDVGIWKAMSKLT KSMCWDLVVIKKD KLNGVGAAIFRKPT SNDCYNNRPQNEPP LCKESDDPNAAWN VPLEACMHKVPED ASVRGSRWPEQWP QRLEKPPYWLNSQ VGVY 448 Pt/POPTR00_02s07640.1 64% 412-629 VILDVGCGVASFGG 788 80% (526/815) YLLEKDVLAMSFA (176/218) PKDEHEAQVQFAL ERGIPAMLAVMGT KRLPFPNSVFDLVH CARCRVPWHIEGG KLLLELNRVLRPGG YFVWSATPVYRKR PEDVGIWKAMSKL TKSMCWDLVVIKT DTLNGVGAAIYRK PTSNDCYNNRPQN EPPLCKESDDPNAA WNVLLEACMHKVP VDASVRGSHWPEQ WPKRLEKPPYWLN SQVGVY 478 Pt/POPTR_0005s06640.1 62% 392-610 VILDVGCGVASFGG 803 75% (499/803) YLFDRDVLAMSFA (166/219) PKDEHEAQIQFALE RGIPAISAVMGTKR LPYPGRVFDAVHC ARCRVPWHIEGGK LLLELNRVLRPGGF FVWSATPVYQKLA EDVEIWQAMTELT KAMCWELVSINKD TLNGVGVATYRKP TSNDCYEKRSKQEP PLCEASDDPNAAW NVPLQACMHKVPV GSLERGSQWPEQW PARLDKTPYWMLS SQVGVY 468 Gm/Glyma04g38870.1 62% 390-608 VILDVGCGVASFGG 798 75% (494/794) FLFDRDVLAMSLAP (165/219) KDEHEAQVQFALE RGIPAISAVMGTKR LPFPGKVFDVVHC ARCRVPWHIEGGK LLLELNRVLRPGGF FVWSATPIYQKLPE DVEIWKAMKTLTK AMCWEVVSISKDQ VNGVGVAVYKKPT SNECYEQRSKNEPP LCPDSDDPNAAWN IKLQACMHKVPASS KERGSKLPELWPA RLTKVPYWLLSSQ VGVY 480 Pt/POPTR_0007s04340.1 61% 420-638 VILDVGCGVASFGG 804 75% (506/829) YLFDRDVLTMSFAP (165/219) KDEHEAQVQFALE RGIPAISAVMGTKR LPYPGRVFDAVHC ARCRVPWHIEGGK LLLELNRVLRPGGL FVWSATPVYQKLA EDVEIWQAMTELT KAMCWELVSINKD TINGVGVATYRKPT SNDCYEKRSKQEPP LCEASDDPNAAWN VPLQACMHKVPVD SLERGSQWPEQWP ARLGKTPYWMLSS QVGVY 428 Si/Si000354m 60% 397-615 VILDVGCGVASFGG 778 75% (486/810) YMFDRDVLTMSFA (166/219) PKDEHEAQVQFAL ERGIPAISAVMGTK RLPYPSRVFDVIHC ARCRVPWHIEGGM LLLELNRLLRPGGY FVWSATPVYQKLP EDVEIWNAMSALT KSMCWKMVNKTK DKLNQVGMAIYQK PMDNNCYEKRSEN NPPLCKDSDDADA AWNVPLEACMHKL PAGPTVRGAKWPE SWPQRLEKTPFWL NGSQVGVY 466 Eg/Eucgr.I00186.1 59% 410-628 VILDVGCGVASFGG 797 75% (487/819) YLFDRDVLAMSLA (165/219) PKDEHEAQVQFAL ERGIPAISAVMGTT RLPFPSRVFDIVHC ARCRVPWHIEGGK LLLELNRLLRPGGF FVWSATPVYQKIPD DVAIWKAMSALLK SMCWELISINKDTL NGVGVATYRKPMS NECYEKRSQNDPP MCADSDDSNAAW YVPLQTCMHKIPID SAERGSQWPEEWP ARLVKTPYWLLSS QVGVY 470 Gm/Glyma06g16050.1 62% 402-620 VILDVGCGVASFGG 799 74% (503/810) FLFDRDVLAMSLAP (164/219) KDEHEAQVQFALE RGIPAISAVMGTKR LPFPGKVFDVVHC ARCRVPWHIEGGK LLLELNRVLRPGGF FVWSATPIYQKLPE DVEIWKAMKALTK AMCWEVVSISKDP VNGVGVAVYRKPT SNECYEQRSKNEPP LCPDSDDPNAAWN IQLQACLHKAPVSS KERGSKLPELWPA RLIKVPYWLSSSQV GVY 482 Vv/GSVIVT01026451001 61% 357-575 VVLDVGCGVASFG 805 74% (480/775) GYLFDKDVLTMSF (164/219) APKDEHEAQVQFA LERGIPGISAVMGT KRLPFPAMVFDVV HCARCRVPWHIEG GKLLLELNRVLRPG GFFVWSATPVYQK LADDVAIWNAMTE LMKSMCWELVVIK RDVVNRVAAAIYK KPTSNDCYEKRSQ NEPPICADSEDANA AWNVPLQACMHK VPVDASKRGSQWP ELWPARLDKSPYW LTSSQVGVY 452 Eg/Eucgr.F04285.1 55% 423-639 VILDVGCGVASFGG 790 74% (465/832) YLFERDVLTMSFAP (162/218) KDVHEAQVQFALE RGIPAILGVMGTKR LPFPGGVFDVIHCA RCRVPWHIEGGKL LLELNRVLRPGGYF LWSATPIYRRDQED IGIWKEMSKLTMA MCWDLVMIKKDK LNKVAIAMYRKPT SNECYEKRPQNEPP LCDNFDDPNSAWN VTLQACMHKVPVD MSKRGSNWPEKWP VRLEKPPYWLNEL GVY 460 Vv/GSVIVT01008776001 73% 150-368 VILDVGCGVASFGG 794 73% (409/554) YIFERDVLAMSFAP (162/219) KDEHEAQVQFALE RGIPAISAVMGTTR LPFPSRVFDVVHCA RCRVPWHIEGGKL LLELNRVLRPGGYF VWSATPVYRKVPE DVGIWNAMSEITK KICWDLVAMSKDS LNGIGAAIYRKPTS NECYEKRPRNEPPL CEESDNADAAWNI PLQACMHKVPVLT SERGSQWPEQWPL RVEKAPNWLKSSQ VGVY 462 Sl/Solyc04g063230.2.1 59% 364-582 VILDVGCGVASFGG 795 73% (470/784) YLFERDVLAMSLA (162/219) PKDEHEAQVQFAL ERGIPAISAVMGTK RLPFPGKVFDAVHC ARCRVPWHIEGGK LLLELNRVLRPGGH FIWSATPVYRKDEE NVGIWEAMSELTK SMCWELLEINEDKL NEVGVAIFRKPTTN DCYQSRTQNDPPM CEEADDPDAAWNI TLQACLHKAPADA SARGAKWPAKWPL RSEKLPYWLKSSQ VGVY 426 Zm/GRMZM2G049269_T01 59% 392-610 VILDVGCGVASFGG 777 73% (479/801) YMFDRDALTMSFA (160/219) PKDEHEAQVQFAL ERGIPAISAVMGTK RLPYPSRVFDVIHC ARCRVPWHIEGGM LLLELNRLLRPGGY FVWSATPVYQKLP EDVEIWNAMSTLT KSMCWKMVNKTK DKLNQVGMVIYQK PMDNICYEKRSENS PPLCKESDDADAA WNVPLEACMHKLP GGSKVRGSKWPEL WPQRLEKTPFWID GSKVGVY 476 Sl/Solyc05g056580.2.1 59% 409-627 VILDVGCGVASFGG 802 73% (486/818) YLFERDVLAMSLA (160/219) PKDEHEAQVQFAL ERGIPAISAVMGTK RLPFPSRVFDVVHC ARCRVPWHIEGGK LLLELNRVLRPGGL FVWSATPVYQKLP EDVEIWEAMQKLT KAMCWDLVSKTK DRVNGVGVAVYR KPTSNECYEQRSKD APPICQGSDDPNAA WNVPLQACMHKA PVATSERGSQWPEP WPARLSKSPYWLL SSQVGVY 474 Gm/Glyma08g00320.1 58% 438-656 VILDVGCGVASFGG 801 73% (493/847) FLFERDVLTMSLAP (162/219) KDEHEAQVQFALE RGIPAISAVMGTKR LPYPGRVFDVVHC ARCRVPWHIEGGK LLLELNRVLRPGGF FVWSATPIYQKLPE DVEIWNEMKALTK AMCWEVVSISKDK LNGVGIAVYKKPTS NECYEKRSQNQPPI CPDSDDPNAAWNV PLQACMHKVPVSS TERGSQWPEKWPA RLTNIPYWLTNSQV GVY 472 Gm/Glyma05g32670.1 58% 427-645 VILDVGCGVASFGG 800 73% (492/837) FLFERDVLTMSLAP (161/219) KDEHEAQVQFALE RGIPAISAVMGTKR LPYPGRVFDVVHC ARCRVPWHIEGGK LLLELNRVLRPGGF FVWSATPIYQKLPE DVEIWNEMKALTK AMCWEVVSISKDK LNGVGIAVYKKPTS NECYEKRSQNQPPI CPDSDDPNAAWNIP LQACMHKVPVSST ERGSQWPEKWPAR LTNTPYWLTNSQV GVY 456 Gm/Glyma04g42270.1 56% 429-646 VILDVGCGVASFGG 792 73% (473/835) YLFEKDVLTMSFAP (160/218) KDVHEAQVQFALE RGIPATLGVMGTV RLPYPGSVFDLVHC ARCRVPWHIEGGK LLLELNRVLRPGGH FVWSATPVYQKDP EDVEIWKAMGEIT KSMCWDLVVIAKD KLNGVAAAIYRKP TDNECYNNRIKHEP PMCSESDDPNTAW NVSLQACMHKVPV DASERGSIWPEQWP LRLEKPPYWIDSQA GVY 422 Bd/Bradi2g57087.1 59% 394-612 VILDVGCGVASFGG 775 72% (485/810) YMFDRDVLTMSFA (158/219) PKDEHEAQVQFAL ERGIPAISAVMGTK RLPYPSRVFDVIHC ARCRVPWHIEGGK LLLELNRLLRPGGY FVWSATPVYQKLP EDVEIWNAMSSLT KSMCWKMVKKTK DTLNQVGMAIYQK PMDNNCYEKRSED SPPLCKETDDADAS WNITLQACIHKLPV GPSVRGSKWPEFW PQRLEKTPFWIDGS HVGVY 424 Os/LOC_Os01g66110.1 58% 406-624 VILDVGCGVASFGG 776 72% (479/812) YMFERDVLTMSFA (159/219) PKDEHEAQVQFAL ERGIPAISAVMGTK RLPYPSRVFDVIHC ARCRVPWHIEGGM LLLELNRLLRPGGY FVWSATPVYQKLP EDVEIWNAMSSLT KAMCWKMVNKTK DKLNQVGMAIYQK PMDNSCYEKRPEN SPPLCKETDDADAA WNVPLQACMHKLP AGQSVRGSKWPET WPQRLEKTPYWID DSHVGIY 464 At/AT5G64030.1 58% 425-643 VVLDVGCGVASFG 796 72% (490/834) GFLFDRDVITMSLA (159/219) PKDEHEAQVQFAL ERGIPAISAVMGTT RLPFPGRVFDIVHC ARCRVPWHIEGGK LLLELNRVLRPGGF FVWSATPVYQKKT EDVEIWKAMSELIK KMCWELVSINKDTI NGVGVATYRKPTS NECYKNRSEPVPPI CADSDDPNASWKV PLQACMHTAPEDK TQRGSQWPEQWPA RLEKAPFWLSSSQT GVY 458 Gm/Glyma06g12540.1 57% 406-623 VILDVGCGVASFGG 793 72% (464/811) YLFEKDVLTMSFAP (159/218) KDVHEAQVQFALE RGIPATLGVMGTV RLPYPGSVFDLLHC ARCRVPWHVEGGK LLLELNRVLRPGGY FVWSATPVYQKDP EDVEIWKAMGEIT KSMCWDLVVIAKD KLNGVAAAIYRKP TDNECYNNRIKNEP SMCSESDDPNTAW NVSLQACMHKVPV DASERGSIWPEQWP LRLEKPPYWIDSQA GVY 438 Bd/Bradi4g23610.1 50% 469-688 VVLDVGCGVASFG 783 70% (440/868) GFLFDRGALTMSFA (155/220) PKDEHEAQVQFAL ERGIPALSAVMGTK RLPFPAGVFDVVHC ARCRVPWHIDGGM LLLELNRLLRPGGF FVWSATPVYQKLP EDVEIWDDMVKLT KAMCWEMVKKTE DTLDQVGLVIFRKP KSNRCYETRRQKEP PLCDGSDDPNAAW NIKLRACMHRAPA DYPSVRGSRWPAP WPERAEAVPYWLN NSQVGVY 434 Zm/GRMZM2G002642_T02 69% 271-489 VVLDVGCGVASFG 781 69% (387/557) GYLFDRDVITMSFA (152/219) PKDEHEAQVQFAL ERGIPAISAVMGTK RLPFPSRVFDVVHC ARCRVPWHIEGGK LLLELDRLLRPGGY FVWSATPVYQKLP EDVEIWQAMSALT SSMCWKMVNKVK DRVNRVGIAIYRKP TDNSCYEARSETNP PLCGEYDDPDAAW NISLGACMHKLPV DPTVRGSQWPELW PLRLEKPPYWLRGS EAGVY 440 Os/LOC_Os11g08314.1 57% 468-686 VALDVGCGVASFG 784 69% (418/726) GYLFDHDVLTMSL (153/219) APKDEHEAQVQFA LERGIPAISAVMGT RRLPFPSNVFDAVH CARCRVPWHIEGG MLLLELNRLLRPGG FFVWSATPVYQELP EDVEIWGEMVKLT KAMCWEMVSKTS DTVDQVGLVTFRK PADNACYMKRRQK EPPLCEPSDDPNAA WNITLRACMHWVP TDPSVRGSWWPER WPERMEKTPYWLN SSQVGVY 430 Bd/Bradi5g27590.1 55% 319-537 VVLDVGCGVASFG 779 69% (429/773) GYLFDRDVLTMSF (153/219) APKDEHEAQVQFA LERGIPAISAVMGT KRLPFPGRVFDAVH CARCRVPWHIEGG KLLLELDRLLRPGG YFVWSATPAYQKL PEDVEIWQAMSAL TRSMCWKMVNKV KDRLNRVGVAIFQ KPIDNRCYDGRSAA NLPLCGEYDNVDA AWNVSLESCIHKLP VDPAIRSSRWPEEW PLRLERAPYWLKSS EPGVY 454 Eg/Eucgr.F04286.1 54% 407-624 VILDVGCGVGSFGG 791 69% (441/813) YLFERDVLTMSFAP (152/219) KDEHEAQVQFALE RGIPAMLAVMGTK RLPFPSGVFDAIHC ARCRVPWHIEGGK LLLELNRLLRPGGY FVWSATPIYRKGPE DLGIWKEMSKLTT AMCWNFTLIKRKD KMNKVSIALYRKP TSNECIESRTKNEPP LCNGLDDANSTWN VTLQACMHKVPTD MSERGSQWPENWL HRLGKPPYWLNKV AVN 442 Si/Si028042m 51% 434-654 VVLDVGCGVASFG 785 69% (436/840) GYLFDRDVLTMSL (154/221) APKDEHEAQVQFA LERGIPAISAVMGT RRLPFPGGVFDVVH CARCRVPWHIDGG MLLLELNRLLRPGG VFVWSATPVYQKL PDDVEIWDEMAKL TKAMCWEMVAKT KHTVVDDQVGVAI FRKPERNGCYEKRP EKAPPLCEPSDDPN AAWNIKLRACMHR VPEDPSERGARWPE PWPERLGKAPYWL DGSQTGVY 432 Os/LOC_Os04g59590.1 65% 275-493 VVLDVGCGVASFG 780 68% (393/599) GYLFDRDVLTMSF (151/219) APKDEHEAQVQFA LERGIPAMSAVMG TKRLPFPGRVFDVV HCARCRVPWHIEG GKLLLELDRLLRPG GYFVWSATPVYQK LPEDVEIWEAMSTL TRSMCWEMVNKV KDRVNRVGIAIFRK PTDNSCYEARSAA NPPICGEYDDPDAA WNISLQSCVHRLPT DPAIRGSQWPVEW PLRLEKPPYWLKNS EAGVY 436 Si/Si021320m 55% 337-555 VVLDVGCGVASFG 782 68% (432/776) GYLFDRDVITMSFA (150/219) PKDEHEAQVQFAL ERGIPAISAVMGTK RLPFPSRVFDVVHC ARCRVPWHIEGGK LLLELDRLLRPGGY FVWSATPVYQKLP EDVEIWEAMSALT RSMCWKMVNKVK DRVNRVGIAIFRKP TDNSCYEERSEANS PICGEYDDPDAAW NVSLRTCMHKLPV DLTIRGSKWPELWP LRLEKPPYWLKSSE AGVY

These functionally-related and/or closely-related PMT24 clade polypeptides may be identified by a consensus methyltransferase domain sequence, SEQ ID NO: 861:

VX²LDVGCGVASFGGX¹⁵X¹⁶FX¹⁸X¹⁹X²⁰X²¹X²²X²³X²⁴SX²⁶APKDX³¹HEAQVQFALERGIPAX⁴⁷X⁴⁸X⁴⁹VMGTX⁵⁴RLPX⁵⁸PX⁶⁰X⁶¹VFDX⁶⁵X⁶⁶HCARCRVPWHX⁷⁷X⁷⁸GGX⁸¹LLLELX⁸⁷RX⁸⁹LRPGGX⁹⁵FX⁹⁷WSATPX¹⁰³YX¹⁰⁵X¹⁰⁶X¹⁰⁷X¹⁰⁸X¹⁰⁹X¹¹⁰X¹¹¹X¹¹²IWX¹¹⁵X¹¹⁶MX¹¹⁸X¹¹⁹X¹²⁰X¹²¹X¹²²X¹²³MCWX¹²⁷X¹²⁸X¹²⁹X¹³⁰X¹³¹X¹³²X¹³³X¹³⁴X¹³⁵X¹³⁶X¹³⁷X¹³⁸X¹³⁹X¹⁴⁰VX¹⁴²X¹⁴³X¹⁴⁴X¹⁴⁵X¹⁴⁶X¹⁴⁷KPX¹⁵⁰X¹⁵¹N X¹⁵³CYX¹⁵⁶X¹⁵⁷RX¹⁵⁹X¹⁶⁰X¹⁶¹X¹⁶²X¹⁶³X¹⁶⁴X¹⁶⁵CX¹⁶⁷X¹⁶⁸X¹⁶⁹DX¹⁷¹X¹⁷²X¹⁷³X¹⁷⁴X¹⁷⁵WX¹⁷⁷X¹⁷⁸X¹⁷⁹LX¹⁸¹X¹⁸²CX¹⁸⁴HX¹⁸⁶X¹⁸⁷X¹⁸⁸X¹⁸⁹X¹⁹⁰X¹⁹¹X¹⁹²X¹⁹³X¹⁹⁴RX¹⁹⁶X¹⁹⁷X¹⁹⁸X¹⁹⁹PX²⁰¹X²⁰²WPX²⁰⁵RX²⁰⁷X²⁰⁸X²⁰⁹X²¹⁰PX²¹²WX²¹⁴X²¹⁵X²¹⁶SX²¹⁸X²¹⁹GX²²¹Y, where X²=any amino acid; X¹⁵=F or Y; X¹⁶=I, L, V or M; X¹⁸=D or E; X¹⁹=H, K or R; X²⁰=D or G; X²¹=any amino acid; X²²=I, L, V or M; X²³=A or T; X²⁴=I, L, V or M; X²⁶=F, I, L, V or M; X³¹=any amino acid; X⁴⁷=T, I, L, V or M; X⁴⁸=any amino acid; X⁴⁹=any amino acid; X⁵⁴=I, L, V or M; X⁵⁸=F or Y; X⁶⁰=A, S or G; X⁶¹=any amino acid; X⁶⁵=I, L, V or M; X⁶⁶=I, L, V or M; X⁷⁷=I, L, V or M; X⁷=D or E; X⁸¹=any amino acid; X⁸⁷=N or D; X⁸⁹=A, I, L, V or M; X⁹⁵=any amino acid; X⁹⁷=I, L, V or M; X¹⁰³=A, I, L, V, or M; X¹⁰⁶=Q or R; X¹⁰⁶=any amino acid; X¹⁰⁷=any amino acid; X¹⁰⁸=any amino acid; X¹⁰⁹=D or E; X¹¹⁰=D or N; X¹¹¹=any amino acid; X¹¹²=any amino acid; X¹¹⁵=any amino acid; X¹¹⁶=any amino acid; X¹¹⁸=any amino acid; X¹¹⁹=any amino acid; X¹²⁰=I, L, V or M; X¹²¹=T, I, L, V or M; X¹²²=any amino acid; X¹²³=any amino acid; X¹²⁷=any amino acid; X¹²⁸=I, L, V or M; X¹²⁹=I, L, V or M; X¹³⁰=any amino acid; X¹³¹=any amino acid; X¹³²=any amino acid; X¹³³=any amino acid; X¹³⁴=H, D; X¹³⁵=any amino acid; X¹³⁶=I, L, V or M; X¹³⁷=V or absent; X¹³⁸=D or absent; X¹³⁹=I, L, V or M; X¹⁴⁰=any amino acid; X¹⁴²=A or G; X¹⁴³=any amino acid; X¹⁴⁴=any amino acid; X¹⁴⁵=T, I, L, V or M; X¹⁴⁶=F or Y; X¹⁴⁷=Q, R or K; X¹⁵⁰=any amino acid; X¹⁵¹=any amino acid; X¹⁵³=any amino acid; X¹⁵⁶=any amino acid; X¹⁵⁷=any amino acid; X¹⁵⁹=any amino acid; X¹⁶⁰=any amino acid; X¹⁶¹=any amino acid; X¹⁶²=any amino acid; X¹⁶³=any amino acid; X¹⁶⁴=S or P; X¹⁶⁵=I, L, V or M; X¹⁶⁷=any amino acid; X¹⁶⁸=any amino acid; X¹⁶⁹=any amino acid; X¹⁷¹=N or D; X¹⁷²=any amino acid; X¹⁷³=N or D; X¹⁷⁴=A or T; X¹⁷⁵=A or S; X¹⁷⁷=any amino acid; X¹⁷⁸=I, L, V or M; X¹⁷⁹=any amino acid; X¹⁸¹=any amino acid; X¹⁸²=A, S or T; X¹⁸⁴=I, L, V or M; X¹⁸⁶=any amino acid; X¹⁸⁷=A, I, L, V or M; X¹⁸⁸=any amino acid; X¹⁸⁹=any amino acid; X¹⁹⁰=any amino acid; X¹⁹¹=Y or absent; X¹⁹²=any amino acid; X¹⁹³=any amino acid; X¹⁹⁴=any amino acid; X¹⁹⁶=S or G; X¹⁹⁷=S or A; X¹⁹⁸=any amino acid; X¹⁹⁹=any amino acid; X²⁰¹=any amino acid; X²⁰²=any amino acid; X²⁰⁵=any amino acid; X²⁰⁷=any amino acid; X²⁰⁸=any amino acid; X²⁰⁹=any amino acid; X²¹⁰=any amino acid; X²¹²=any amino acid; X²¹⁴=I, L, V or M; X²¹⁵=any amino acid; X²¹⁶=any amino acid or absent; X²¹⁸=K, E, H or Q; X²¹⁹=any amino acid; and X²²¹=I, L, V or M.

Alternative consensus sequences comprising the above with conservative substitutions found in the instant Tables are also envisaged and may be expected to provide equivalent function(s).

The presence of one or more of these consensus sequences and/or these amino acid residues is correlated with conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. An AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide sequence that is “functionally-related and/or closely-related” to the listed full length protein sequences or domains provided in the instant Tables may also have, to any of the listed sequences found in the Sequence Listing or to the entire length of a listed sequence, at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to any of SEQ ID NOs: 2, 42, 86, 108, 126, 156, 192, 246, 278, 318, 356, 388, 410, 444 or SEQ ID NOs: 2n where n=1 to 241, and/or at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to a domain of any of SEQ ID NOs: 483, 490, 510, 538, 566, 588, 599, 608, 623, 629, 659, 686, 702, 721, 741, 760, 769, 786, 813, and/or at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or about 100% identity to any of consensus sequences SEQ ID NOs: 842-861. The presence of the listed domains in a listed polypeptide sequence is correlated with the conferring of improved or increased photosynthetic resource use efficiency to a plant when the expression level of the polypeptide is altered in a plant by being reduced, knocked-out, or overexpressed. All of the sequences that adhere to these functional and sequential relationships are herein referred to as AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptides, or which fall within the AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade exemplified in the phylogenetic trees presented in the Figures.

Example II. Plant Genotypes and Vector and Cloning Information

A variety of constructs may be used to modulate the activity of regulatory polypeptides (RPs), and to test the activity of orthologs and paralogs in transgenic plant material. This platform provides the material for all subsequent analysis.

An individual plant “genotype” refers to a set of plant lines containing a particular construct or knockout (for example, this might be 35S lines for a given gene sequence (GID, Gene Identifier) being tested, 35S lines for a paralog or ortholog of that gene sequence, lines for an RNAi construct, lines for a GAL4 fusion construct, or lines in which expression of the gene sequence is driven from a particular promoter that enhances expression in particular cell, tissue or condition). For a given genotype arising from a particular transformed construct, multiple independent transgenic lines may be examined for morphological and physiological phenotypes. Each individual “line” (also sometimes known as an “event”) refers to the progeny plant or plants deriving from the stable integration of the transgene(s), carried within the T-DNA borders contained within a transformation construct, into a specific location or locations within the genome of the original transformed cell. It is well known in the art that different lines deriving from transformation with a given transgene may exhibit different levels of expression of that transgene due to so called “position effects” of the surrounding chromatin at the locus of integration in the genome, and therefore it is necessary to examine multiple lines containing each construct of interest.

(1) Overexpression/Tissue-Enhanced/Conditional Expression.

Expression of a given regulatory protein from a particular promoter, for example a photosynthetic tissue-enhanced promoter (e.g., a green tissue- or leaf-enhanced promoter), is achieved either by a direct-promoter fusion construct in which that regulatory protein is cloned directly behind the promoter of interest or by a two component system.

The Two-Component Expression System.

For the two-component system, two separate constructs are used: Promoter::LexA-GAL4TA and opLexA::RP. The first of these (Promoter::LexA-GAL4TA) comprises a desired promoter cloned in front of a LexA DNA binding domain fused to a GAL4 activation domain. The construct vector backbone (pMEN48, also known as P5375) also carries a kanamycin resistance marker, along with an opLexA::GFP (green fluorescent protein) reporter. Transgenic lines are obtained containing this first component, and a line is selected that shows reproducible expression of the reporter gene in the desired pattern through a number of generations. A homozygous population is established for that line, and the population is supertransformed with the second construct (opLexA::RP) carrying the regulatory protein of interest cloned behind a LexA operator site. This second construct vector backbone (pMEN53, also known as P5381) also contains a sulfonamide resistance marker.

Conditional Expression.

Various promoters can be used to overexpress disclosed polypeptides in plants to confer improved photosynthetic resource use efficiency. However, in some cases, there may be limitations in the use of various proteins that confer increased photosynthetic resource use efficiency when the proteins are overexpressed. Negative side effects associated with constitutive overexpression such as small size, delayed growth, increased disease sensitivity, and development and alteration in flowering time are not uncommon. A number of stress-inducible promoters can be used promote protein expression during the periods of stress, and therefore may be used to induce overexpression of polypeptides that can confer improved stress tolerance when they are needed without the adverse developmental or morphological effects that may be associated with their constitutive overexpression.

Promoters that drive protein expression in response to stress can be used to regulate the expression of the disclosed polypeptides to confer photosynthetic resource use efficiency to plants. The promoter may regulate expression of a disclosed polypeptide to an effective level in a photosynthetic tissue. Effective level in this regard refers to an expression level that confers greater photosynthetic resource use efficiency in the transgenic plant relative to the control plant that, for example, does not comprise a recombinant polynucleotide that encodes the disclosed polypeptide. Optionally, the promoter does not regulate protein expression in a constitutive manner.

Such promoters include, but are not limited to, the sequences located in the promoter regions of At5g52310 (RD29A), At5g52300, AT1G16850, At3g46230, AT1G52690, At2g37870, AT5G43840, At5g66780, At3g17520, and At4g09600.

In addition, promoters with expression specific to or enhanced in particular cells or tissue types may be used to express a given regulatory protein only in these cells or tissues. Examples of such promoter types include but are not limited to promoters expressed in green tissue, guard cell, epidermis, whole root, root hairs, vasculature, apical meristems, and developing leaves.

Table 22 lists a number of photosynthetic tissue-enhanced promoters, specifically, mesophyll tissue-enhanced promoters from rice, that may be used to regulate expression of polynucleotides and polypeptides found in the Sequence Listing and structurally and functionally-related sequences. Promoters that may be used to drive expression of polynucleotides and polypeptides found in the Sequence Listing and structurally and functionally-related sequences included, but are not limited to, promoter sequences SEQ ID NO: 862-864 and the following promoters listed in Table 22, as well as promoters that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to SEQ ID NO: 862-888, or comprise a functional fragment of promoters that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% identical to SEQ ID NO: 862-888.

TABLE 22 Rice Genes with Photosynthetic Tissue-Enhanced Promoters Rice Gene Identifier of Photosynthetic SEQ ID NO: Tissue-Enhanced Promoter 865 Os02g09720 866 Os05g34510 867 Os11g08230 868 Os01g64390 869 Os06g15760 870 Os12g37560 871 Os03g17420 872 Os04g51000 873 Os01g01960 874 Os05g04990 875 Os02g44970 876 Os01g25530 877 Os03g30650 878 Os01g64910 879 Os07g26810 880 Os07g26820 881 Os09g11220 882 Os04g21800 883 Os10g23840 884 Os08g13850 885 Os12g42980 886 Os03g29280 887 Os03g20650 888 Os06g43920

Tissue-enhanced promoters that may be used to drive expression of polynucleotides and polypeptides found in the Sequence Listing and structurally and functionally-related sequences have also been described in U.S. patent publication no. 20110179520A1, incorporated herein by reference. Such promoters include, but are not limited to, Arabidopsis sequences located in the promoter regions of AT1G08465, AT1G10155, AT1G14190, AT1G24130, AT1G24735, AT1G29270, AT1G30950, AT1G31310, AT1G37140, AT1G49320, AT1G49475, AT1G52100, AT1G60540, AT1G60630, AT1G64625, AT1G65150, AT1G68480, AT1G68780, AT1G69180, AT1G77145, AT1G80580, AT2G03500, AT2G17950, AT2G19910, AT2G27250, AT2G33880, AT2G39850, AT3G02500, AT3G12750, AT3G15170, AT3G16340, AT3G27920, AT3G30340, AT3G42670, AT3G44970, AT3G49950, AT3G50870, AT3G54990, AT3G59270, AT4G00180, AT4G00480, AT4G12450, AT4G14819, AT4G31610, AT4G31615, AT4G31620, AT4G31805, AT4G31877, AT4G36060, AT4G36470, AT4G36850, AT4G37970, AT5G03840, AT5G12330, AT5G14070, AT5G16410, AT5G20740, AT5G27690, AT5G35770, AT5G39330, AT5G42655, AT5G53210, AT5G56530, AT5G58780, AT5G61070, and AT5G6491.

In addition to the sequences provided in the Sequence Listing or in this Example, a promoter region may include a fragment of the promoter sequences provided in the Sequence Listing or in this Example, or a complement thereof, wherein the promoter sequence, or the fragment thereof, or the complement thereof, regulates expression of a polypeptide in a plant cell, for example, in response to a biotic or abiotic stress, or in a manner that is enhanced or preferred in certain plant tissues.

(2) Knock-Out/Knock-Down

In some cases, lines mutated in a given regulatory protein may be analyzed. Where available, T-DNA insertion lines in a given gene are isolated and characterized. In cases where a T-DNA insertion line is unavailable, an RNA interference (RNAi) strategy is sometimes used.

Example III. Transformation Methods

Crop species that overexpress polypeptides of the instant description may produce plants with increased photosynthetic resource use efficiency and/or yield. Thus, polynucleotide sequences listed in the Sequence Listing recombined into, for example, one of the expression vectors of the instant description, or another suitable expression vector, may be transformed into a plant for the purpose of modifying plant traits for the purpose of improving yield, quality, and/or photosynthetic resource use efficiency. The expression vector may contain a constitutive, tissue-enhanced or inducible promoter operably linked to the polynucleotide. The cloning vector may be introduced into a variety of plants by means well known in the art such as, for example, direct DNA transfer or Agrobacterium tumefaciens-mediated transformation.

Transformation of Monocots.

Cereal plants including corn, wheat, rice, sorghum, barley, or other monocots may be transformed with the present polynucleotide sequences, including monocot or eudicot-derived sequences such as those presented in the present Tables, cloned into a vector such as pGA643 and containing a kanamycin-resistance marker, and expressed constitutively under, for example, the CaMV35S or COR15 promoters, or with tissue-enhanced or inducible promoters. The expression vectors may be one found in the Sequence Listing, or any other suitable expression vector may be similarly used. For example, pMEN020 may be modified to replace the NptII coding region with the BAR gene of Streptomyces hygroscopicus that confers resistance to phosphinothricin. The Kpnl and BglII sites of the Bar gene are removed by site-directed mutagenesis with silent codon changes.

The cloning vector may be introduced into a variety of cereal plants by means well known in the art including direct DNA transfer or Agrobacterium tumefaciens-mediated transformation. The latter approach may be accomplished by a variety of means, including, for example, that of U.S. Pat. No. 5,591,616, in which monocotyledon callus is transformed by contacting dedifferentiating tissue with the Agrobacterium containing the cloning vector.

The sample tissues are immersed in a suspension of 3×10⁻⁹ cells of Agrobacterium containing the cloning vector for 3-10 minutes. The callus material is cultured on solid medium at 25° C. in the dark for several days. The calli grown on this medium are transferred to a Regeneration Medium. Transfers are continued every two to three weeks (two or three times) until shoots develop. Shoots are then transferred to Shoot-Elongation Medium every 2-3 weeks. Healthy looking shoots are transferred to Rooting Medium and after roots have developed, the plants are placed into moist potting soil.

The transformed plants are then analyzed for the presence of the NPTII gene/kanamycin resistance by ELISA, using the ELISA NPTII kit from 5Prime-3Prime Inc. (Boulder, Colo.).

It is also routine to use other methods to produce transgenic plants of most cereal crops (Vasil, 1994. Plant Mol. Biol. 25: 925-937) such as corn, wheat, rice, sorghum (Cassas et al., 1993. Proc. Natl. Acad. Sci. USA 90: 11212-11216), and barley (Wan and Lemeaux, 1994. Plant Physiol. 104: 37-48). DNA transfer methods such as the microprojectile method can be used for corn (Fromm et al., 1990. Bio/Technol. 8: 833-839; Gordon-Kamm et al., 1990. Plant Cell 2: 603-618; Ishida, 1990. Nature Biotechnol. 14:745-750), wheat (Vasil et al., 1992. Bio/Technol. 10:667-674; Vasil et al., 1993. Bio/Technol. 11:1553-1558; Weeks et al., 1993. Plant Physiol. 102:1077-1084), and rice (Christou, 1991. Bio/Technol. 9:957-962; Hiei et al., 1994. Plant J. 6:271-282; Aldemita and Hodges, 1996. Planta 199: 612-617; and Hiei et al., 1997. Plant Mol. Biol. 35:205-218). For most cereal plants, embryogenic cells derived from immature scutellum tissues are the preferred cellular targets for transformation (Hiei et al., 1997. supra; Vasil, 1994. supra). For transforming corn embryogenic cells derived from immature scutellar tissue using microprojectile bombardment, the A188XB73 genotype is the preferred genotype (Fromm et al., 1990. Bio/Technol. 8: 833-839; Gordon-Kamm et al., 1990. supra). After microprojectile bombardment the tissues are selected on phosphinothricin to identify the transgenic embryogenic cells (Gordon-Kamm et al., 1990. supra). Transgenic plants from transformed host plant cells may be regenerated by standard corn regeneration techniques (Fromm et al., 1990. Bio/Technol. 8: 833-839; Gordon-Kamm et al., 1990. supra).

Transformation of Dicots.

It is now routine to produce transgenic plants using most eudicot plants (see U.S. Pat. No. 8,273,954 (Rogers et al.) issued Sep. 25, 2012; Weissbach and Weissbach, 1989. Methods for Plant Molecular Biology, Academic Press; Gelvin et al., 1990. Plant Molecular Biology Manual, Kluwer Academic Publishers; Herrera-Estrella et al., 1983. Nature 303: 209; Bevan, 1984. Nucleic Acids Res. 12: 8711-8721; and Klee, 1985. Bio/Technology 3: 637-642). Methods for analysis of traits are routine in the art and examples are disclosed above.

Numerous protocols for the transformation of tomato and soy plants have been previously described, and are well known in the art. Gruber et al., in Glick and Thompson, 1993. Methods in Plant Molecular Biology and Biotechnology. eds., CRC Press, Inc., Boca Raton, describe several expression vectors and culture methods that may be used for cell or tissue transformation and subsequent regeneration. For soybean transformation, methods are described by Miki et al., 1993. in Methods in Plant Molecular Biology and Biotechnology, p. 67-88, Glick and Thompson, eds., CRC Press, Inc., Boca Raton; and U.S. Pat. No. 5,563,055, (Townsend and Thomas), issued Oct. 8, 1996.

There are a substantial number of alternatives to Agrobacterium-mediated transformation protocols, other methods for the purpose of transferring exogenous genes into soybeans or tomatoes. One such method is microprojectile-mediated transformation, in which DNA on the surface of microprojectile particles is driven into plant tissues with a biolistic device (see, for example, Sanford et al., 1987. Part. Sci. Technol. 5:27-37; Sanford, 1993. Methods Enzymol. 217: 483-509; Christou et al., 1992. Plant. J. 2: 275-281; Klein et al., 1987. Nature 327: 70-73; U.S. Pat. No. 5,015,580 (Christou et al), issued May 14, 1991; and U.S. Pat. No. 5,322,783 (Tomes et al.), issued Jun. 21, 1994).

Alternatively, sonication methods (see, for example, Zhang et al., 1991. Bio/Technology 9: 996-997); direct uptake of DNA into protoplasts using CaCl₂ precipitation, polyvinyl alcohol or poly-L-ornithine (see, for example, Hain et al., 1985. Mol. Gen. Genet. 199: 161-168; Draper et al., 1982. Plant Cell Physiol. 23: 451-458); liposome or spheroplast fusion (see, for example, Deshayes et al., 1985. EMBO J., 4: 2731-2737; Christou et al., 1987. Proc. Natl. Acad. Sci. USA 84: 3962-3966); and electroporation of protoplasts and whole cells and tissues (see, for example, Donn et al. 1990. in Abstracts of VIIth International Congress on Plant Cell and Tissue Culture IAPTC, A2-38: 53; D'Halluin et al., 1992. Plant Cell 4: 1495-1505; and Spencer et al., 1994. Plant Mol. Biol. 24: 51-61) have been used to introduce foreign DNA and expression vectors into plants.

After a plant or plant cell is transformed (and the transformed host plant cell then regenerated into a plant), the transformed plant may propagated vegetatively or it may be crossed with itself or a plant from the same line, a non-transformed or wild-type plant, or another transformed plant from a different transgenic line of plants. Crossing provides the advantages of producing new and often stable transgenic varieties. Genes and the traits they confer that have been introduced into a tomato or soybean line may be moved into distinct line of plants using traditional backcrossing techniques well known in the art. Transformation of tomato plants may be conducted using the protocols of Koornneef et al, 1986. In Tomato Biotechnology: Alan R. Liss, Inc., 169-178, and in U.S. Pat. No. 6,613,962, the latter method described in brief here. Eight day old cotyledon explants are precultured for 24 hours in Petri dishes containing a feeder layer of Petunia hybrida suspension cells plated on MS medium with 2% (w/v) sucrose and 0.8% agar supplemented with 10 μM α-naphthalene acetic acid and 4.4 μM 6-benzylaminopurine. The explants are then infected with a diluted overnight culture of Agrobacterium tumefaciens containing an expression vector comprising a polynucleotide of the instant description for 5-10 minutes, blotted dry on sterile filter paper and cocultured for 48 hours on the original feeder layer plates. Culture conditions are as described above. Overnight cultures of Agrobacterium tumefaciens are diluted in liquid MS medium with 2% (w/v/) sucrose, pH 5.7, to an OD₆₀₀ of 0.8.

Following cocultivation, the cotyledon explants are transferred to Petri dishes with selective medium comprising MS medium with 4.56 μM zeatin, 67.3 μM vancomycin, 418.9 μM cefotaxime and 171.6 μM kanamycin sulfate, and cultured under the culture conditions described above. The explants are subcultured every three weeks onto fresh medium. Emerging shoots are dissected from the underlying callus and transferred to glass jars with selective medium without zeatin to form roots. The formation of roots in a kanamycin sulfate-containing medium is a positive indication of a successful transformation.

Transformation of soybean plants may be conducted using the methods found in, for example, U.S. Pat. No. 5,563,055 (Townsend et al., issued Oct. 8, 1996), described in brief here. In this method soybean seed is surface sterilized by exposure to chlorine gas evolved in a glass bell jar. Seeds are germinated by plating on 1/10 strength agar solidified medium without plant growth regulators and culturing at 28° C. with a 16 hour day length. After three or four days, seed may be prepared for cocultivation. The seedcoat is removed and the elongating radicle removed 3-4 mm below the cotyledons.

Eucalyptus is now considered an important crop that is grown for example to provide feedstocks for the pulp and paper and biofuel markets. This species is also amenable to transformation as described in PCT patent publication WO/2005/032241.

Crambe has been recognized as a high potential oilseed crop that may be grown for the production of high value oils. An efficient method for transformation of this species has been described in PCT patent publication WO 2009/067398 A1.

Overnight cultures of Agrobacterium tumefaciens harboring the expression vector comprising a polynucleotide of the instant description are grown to log phase, pooled, and concentrated by centrifugation. Inoculations are conducted in batches such that each plate of seed was treated with a newly resuspended pellet of Agrobacterium. The pellets are resuspended in 20 ml inoculation medium. The inoculum is poured into a Petri dish containing prepared seed and the cotyledonary nodes are macerated with a surgical blade. After 30 minutes the explants are transferred to plates of the same medium that has been solidified. Explants are embedded with the adaxial side up and level with the surface of the medium and cultured at 22° C. for three days under white fluorescent light. These plants may then be regenerated according to methods well established in the art, such as by moving the explants after three days to a liquid counter-selection medium (see U.S. Pat. No. 5,563,055).

The explants may then be picked, embedded and cultured in solidified selection medium. After one month on selective media transformed tissue becomes visible as green sectors of regenerating tissue against a background of bleached, less healthy tissue. Explants with green sectors are transferred to an elongation medium. Culture is continued on this medium with transfers to fresh plates every two weeks. When shoots are 0.5 cm in length they may be excised at the base and placed in a rooting medium.

Experimental Methods; Transformation of Arabidopsis.

Transformation of Arabidopsis is performed by an Agrobacterium-mediated protocol based on the method of Bechtold and Pelletier, 1998. Unless otherwise specified, all experimental work is performed using the Columbia ecotype.

Plant Preparation.

Arabidopsis seeds are gas sterilized and sown on plates with media containing 80% MS with vitamins, 0.3% sucrose and 1% Bacto™ agar. The plates are placed at 4° in the dark for the days then transferred to 24 hour light at 22° for 7 days. After 7 days the seedlings are transplanted to soil, placing individual seedlings in each pot. The primary bolts are cut off a week before transformation to break apical dominance and encourage auxiliary shoots to form. Transformation is typically performed at 4-5 weeks after sowing.

Bacterial Culture Preparation.

Agrobacterium stocks are inoculated from single colony plates or from glycerol stocks and grown with the appropriate antibiotics until saturation. On the morning of transformation, the saturated cultures are centrifuged and bacterial pellets are re-suspended in Infiltration Media (0.5×MS, 1× Gamborg's Vitamins, 5% sucrose, 200 μl/L Silwet® L77) until an A₆₀₀ reading of 0.8 is reached.

Transformation and Harvest of Transgenic Seeds.

The Agrobacterium solution is poured into dipping containers. All flower buds and rosette leaves of the plants are immersed in this solution for 30 seconds. The plants are laid on their side and wrapped to keep the humidity high. The plants are kept this way overnight at 22° C. and then the pots are turned upright, unwrapped, and moved to the growth racks. In most cases, the transformation process is repeated one week later to increase transformation efficiency.

The plants are maintained on the growth rack under 24-hour light until seeds are ready to be harvested. Seeds are harvested when 80% of the siliques of the transformed plants are ripe (approximately five weeks after the initial transformation). This seed is deemed T₀ seed, since it is obtained from the T₀ generation, and is later plated on selection plates (either kanamycin or sulfonamide). Resistant plants that are identified on such selection plates comprise the T1 generation, from which transgenic seed comprising an expression vector of interest may be derived.

Example IV. Primary Screening Materials and Methods

Plant Growth Conditions.

Seeds from Arabidopsis lines are chlorine gas sterilized using a standard protocol and spread onto plates containing a sucrose-based media augmented with vitamins (80% MS+Vit, 1% sucrose, 0.65% PhytoBlend™ Agar; Caisson Laboratories, Inc., North Logan, Utah) and appropriate kanamycin or sulfonamide concentrations where selection is required. Seeds are stratified in the dark on plates, at 4° C. for 3 days then moved to a walk-in growth chamber (Conviron MTW120, Conviron Controlled Environments Ltd, Winnipeg, Manitoba, Canada) running at a 10 hour photoperiod at a photosynthetic photon flux of approximately 200 μmol m⁻² s⁻¹ at plant height and a photoperiod/night temperature regime of 22° C./19° C. After seven days of light exposure seedlings are transplanted into 164 ml volume pots containing autoclaved ProMix® soil. All pots are returned to the same growth-chamber where they are stood in water and covered with a lid for the first seven days. This protocol keeps the soil moist during this period. Seven days after transplanting lids are removed and a watering and nutrition regime begun. All plants receive water three times a week, and a weekly a fertilizer treatment (80% Peter's NPK fertilizer).

Primary Screening.

Between 35 and 38 days after being transferred to lighted conditions on plates, and after between 28 and 31 days growth in soil, a suite of leaf-physiological parameters are measured using an infrared gas analyzer (LI-6400XT, LI-COR® Biosciences, Lincoln, NB, USA) integrated with a fluorimeter that measures fluorescence from Chlorophyll A (LI-6400-40, LI-COR Biosciences). This technique involves clamping a leaf between two gaskets, effectively sealing it inside a chamber, then measuring the exchange of carbon dioxide and water vapor between the leaf and the air flowing through the chamber. This gas exchange is monitored simultaneously with the fluorescence levels from the chlorophyll a molecules in the leaf. The growth conditions used, and plant age and leaf selection criteria for measurement are designed to maximize the chance that the leaves sampled fill the 2 cm² leaf chamber of the gas-exchange system and that plants show no visible signs of having transitioned to reproductive growth.

Screening High-Light Leaf Physiology at Two Air Temperatures.

Leaf physiology is screened after plants have been acclimated to high light (700 μmol photons m⁻² s⁻¹) under LED light banks emitting visible light (400-700 nm, Photon Systems Instruments, Brno, Czech Republic), for 40 minutes. Other than the change in light level, the atmospheric environment is the same as that in which the plants have been grown, and the LI-6400 leaf chamber is set to reflect this, being set to deliver a photosynthetic photon flux of 700 μmol photons m⁻² s⁻¹ and operate at an air temperature of 22° C. Forty minutes acclimation to a photosynthetic photon flux of 700 μmol photons m⁻² s⁻¹ has repeatedly been shown to be sufficient to achieve a steady-state rate of light-saturated photosynthesis and stomatal conductance in control plants. Gas exchange and fluorescence data are logged simultaneously two minutes after the leaf has been closed in the chamber. Two minutes is found to be long enough for the leaf chamber CO₂ and H₂O concentrations to stabilize after closing a new leaf inside, and thereby minimizing leaf physiological adjustment to small differences between the growth environment and the LI-6400 chamber. Screening at the growth air temperature of 22° C. is begun one hour into the photoperiod and is typically completed in two hours. After being screened at 22° C., plants are returned to growth-light levels prior to being screened again at 35° C. later in the photoperiod. The higher-temperature screening begins six hours into the photoperiod and measurements are made after the rosettes have been acclimated to the same high light dose as described above, but this time in a controlled environment with an air temperature set to 35° C. Measurements are again made in a leaf chamber set to match the warmer air temperature and logged using the protocol described above for the 22° C. measurements. Data generated at both 22° C. and 35° C. are used to calculate: rates of CO₂ assimilation by photosynthesis (A, μmol CO₂ m⁻² s⁻¹); rates of H₂O loss through transpiration (Tr, mmol H₂O m⁻² s⁻¹); the conductance to CO₂ and H₂O movement between the leaf and air through the stomatal pore (g_(s), mol. H₂O m⁻² s⁻¹); the sub-stomatal CO₂ concentration (C_(i), μmol CO₂ mol⁻¹); transpiration efficiency, the instantaneous ratio of photosynthesis to transpiration, (TE=A/Tr (μmol CO₂ mmol H₂O m⁻² s⁻¹)); the rate of electron flow through photosystem two (ETR μmol e−m⁻² s⁻¹). Derivation of the parameters described above followed established published protocols (Long & Bernacchi, 2003. J. Exp. Botany; 54:2393-24)

Leaves from up to 10 replicate plants are screened for a given line of interest. Data generated from these lines are compared with that from an empty vector control line planted at the same time, grown within the same flats, and screened at the same time.

For control lines, data are collected not only at an atmospheric CO₂ concentration of 400 μmol CO₂ mol⁻¹, but also after stepwise changes in CO₂ concentration to 350, 300, 450 and 500 μmol CO₂ mol⁻¹. These measurements underlay screening for more complex physiological traits of: (1) photosynthetic capacity; (2) Non-photochemical quenching; and (3) non-photosynthetic metabolism.

Screening Photosynthetic Capacity.

Under most conditions, the rate of light-saturated photosynthesis in a C3 leaf is a product of the biochemical capacity of the Calvin cycle and the transfer conductance of CO₂ concentration to the sites of carboxylation (Farquhar et al., 1980. Planta: 149, 78-90). Plotting the rate of photosynthesis against an estimate of the sub-stomatal CO₂ concentration (C_(i)) provides a means to identify changes in photosynthetic capacity of the Calvin cycle independent of changes in stomatal conductance, a key component of the total transfer conductance to CO₂ of the leaf. Consequently, for lines being screened, rates of photosynthesis are plotted against a regression plot of A vs. C_(i) generated for the control lines over a range of atmospheric CO₂ concentration, as described above. This technique enables visual confirmation of changes in photosynthetic capacity in lines of interest.

Screening Non-Photochemical Quenching.

During acclimation to high light, the efficiency with which photosystem PSII operates will reach a steady state regulated largely by the feedback between non-photochemical quenching (NPQ) in the antenna and the metabolic demand for energy produced in the chloroplast (Genty et al., 1989. Biochim. Biophys. Acta 990:87-92; Baker et al., 2007. Plant Cell Environ. 30:1107-1125). This understanding is used in this screen to identify lines in which the limitation that non-photochemical quenching exerts on the efficiency with which photosystem II operates is decreased or increased. A decrease in non-photochemical quenching may be the consequence of a decrease in the capacity for NPQ. This would result in lower levels of non-photochemical quenching and a higher efficiency of photosynthesis over a range of light levels, but importantly, higher rates of photosynthesis at low light where light-use efficiency is important. However, changes in rate at which NPQ responds to light could also underlie any increases or decreases in NPQ. Of these, an increase in the rate at which NPQ relaxes has the potential to increase rates of photosynthesis as leaves in crop canopies transition from high to low light, and is therefore relevant to increasing crop-canopy photosynthesis (Zhu et al., 2010. Plant Biol. 61:235-261). In keeping with the A/Ci analysis described above, a regression of the operating efficiency of PSII against non-photochemical quenching is generated for the control line from data collected over a range of atmospheric CO₂ concentration. This technique enables visual confirmation of changes in the regulation of PSII operation that are driven by changes in non-photochemical quenching in lines of interest.

Screening for Non-Photosynthetic Metabolism.

Measurement of the ratio of the rate of electron flow through PSII (ETR) to the rate of photosynthesis (A) is used to screen for changes in non-photosynthetic metabolism. This screen is based upon the understanding that the transport of four μmol of electrons from PSII to photosystem one PSI will supply the NADPH and ATP required to fix one μmol of CO₂ in the Calvin cycle. For a C3 leaf operating in an atmosphere with 21% oxygen, the ratio of electron flow to photosynthesis should be higher than four, reflecting photorespiratory and other metabolism. However, because the rate of photorespiration in a C3 leaf is dependent upon the concentration of CO₂ at the active site of Rubisco, a regression of the ratio of electron flow to photosynthesis, generated over the range of CO₂ concentrations described above, provides the reference regression against which lines being screened can be compared to controls. Changes in the ratio of ETR to A, when observed at the same C_(i) as the control line, could indicate changes in the specificity of the Rubisco active site for O₂ relative to CO₂ and or other metabolic sinks which would be expected to have important implications for crop productivity and/or stress tolerance.

Surrogate Screening for Growth-Light Physiology.

Rosette biomass: the dry weight of whole Arabidopsis rosettes (i.e., above-ground biomass) is measured after being dried down at 80° C. for 24 hours, a time found to be sufficient to reach constant weight. Samples are taken after 35-38 days growth, and used as an assay of above-ground productivity at growth light. Typically, five replicate rosettes are sampled per Arabidopsis line being screened.

Rosette chemical and isotopic C and N analysis: after weighing, the five rosettes sampled for each line screened are pooled together and ground to a fine powder. The pooled sample generated is sub-sampled and approximately 4 μg samples are prepared for analysis.

Chlorophyll content index (CCI): measurements of light transmission through the leaf are made for plants being screened using a chlorophyll content meter (CCM-200, Apogee Instruments, Logan, Utah, USA). The first is made within the first hour of the photoperiod prior to any acclimation to high light on leaves of plants samples for rosette analysis. The second is made later in the photoperiod on leaves of plants that had undergone the high-temperature screening.

Light absorption: measurements of CCI are used as a surrogate for leaf light absorption, based upon a known relationship between the two. The estimates of light absorption by the leaf, required to construct this relationship, were made by placing the leaf on top of a quantum sensor (LI-190, LI-COR Biosciences) with both the leaf and quantum sensor then pressed firmly up to the foam gasket underneath the LI-6400 light source. This procedure provides an estimate of the transmission of a known light flux through the leaf and is used to estimate the fraction of light absorbed by the leaf.

Example V. Experimental Results

This Example provides experimental observations for transgenic plants overexpressing AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 related polypeptides assayed for improved photosynthetic resource use efficiency.

The ability of a crop canopy to photosynthesize, and the rate at which it can do this relative to the availability of resources, is an important determinant of crop yield. Consequently, increasing the rate of photosynthesis relative to resources that can limit productivity and yield is considered a pathway to improving crop yield across broad acres.

The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air to sugars, in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthetic capacity is considered a pathway to improving crop yield across broad acres.

Tables 23-35 and the instant Figures provide evidence for improved photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 in experiments conducted to date. All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding an AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24-related polypeptide or overexpress an AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.

Table 23 describes an increased capacity for photosynthesis and increased photosynthetic rate in five independent lines overexpressing AtMYB27. Table 23 describes increased photosynthesis in five out of six independent lines overexpressing MYB27. When averaged for these five MYB27 overexpression lines, photosynthetic rate was increased by 23%. Table 5 also details how for four of these MYB27 overexpression lines this increase in photosynthetic rate is clearly linked to an increase in capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the activity of Rubisco and the capacity to regenerate RuBP in the Calvin cycle are key constraints. FIGS. 3 and 4 display evidence of increases in both Rubisco activity and the capacity to regenerate RuBP in multiple MYB27 overexpression lines (Long & Bernacchi 2003 already cited above, describe the basis for assaying Rubisco activity and RuBP regeneration capacity). For lines 1, 2 and 6, both the activity of Rubisco and the capacity to regenerate RuBP were increased by MYB27 overexpression. For line 5, only an increase in the capacity for RuBP regeneration was observed. Photosynthetic resource use efficiency was also increased in five of the six lines assayed. When averaged for these five lines, the 23% increase in photosynthetic rate was observed in tandem with a smaller, 13% increase in the nitrogen content of the rosette tissue.

TABLE 23 Components of increased photosynthetic resource use efficiency in AtMYB27 overexpression lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis) and rosette nitrogen concentration (rosette [N]). Effects on photosynthetic capacity are also described and where known the biochemical basis for the effect is described as either due to effects on Rubisco activity (Rubisco) or the capacity to regenerate RuBP (RuBP). Polypeptide Sequence/ SEQ Photosynthetic Rosette Line ID NO: Driver Target Photosynthesis Capacity [N] AtMYB27/ 2 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1311 Increased Increased Increased Line 1 (43%) Rubisco and (25%) RuBP AtMYB27/ 2 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1311 Increased Increased Increased Line 2 (30%) Rubisco and (30%) RuBP AtMYB27/ 2 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1311 No effect No effect No effect Line 3 AtMYB27/ 2 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1311 Increased No effect Increased Line 4 (14%) (8%) AtMYB27/ 2 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1311 Increased Increased No effect Line 5 (8%) RuBP AtMYB27/ 2 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1311 Increased Increased Increased Line 6 (20%) Rubisco and (3%) RuBP

The results presented in Table 23 were determined after screening six independent transgenic events. Lines 1 and 2 were screened twice and the effect size reported for a given parameter is the mean of the two screening runs. For both lines the direction of the effect was the same in both runs. Lines 3, 4, 5 and 6 were screened once.

Table 24 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing RBP45A in experiments conducted to date. Table 24 describes increased photosynthesis in five out of six independent lines overexpressing RBP45A. When averaged for these six lines, photosynthetic rate was increased by 11% in the RBP45A overexpression lines. Leaf chlorophyll absorbs light energy utilized for photosynthesis, and was increased by 5% when average across all six lines. Rosette nitrogen content was reduced by 3% in the five lines for which it was measured. That photosynthesis is increased in RBP45A overexpression lines to a greater extent than the investment in chlorophyll, while rosette nitrogen content is decreased, provides evidence that RBP45A overexpression improves the efficiency with which photosynthesis operates relative to availability of the key resources of light and nitrogen.

TABLE 24 Components of increased photosynthetic resource use efficiency in RBP45A overexpression lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), leaf chlorophyll content and rosette nitrogen concentration (rosette [N]). Polypeptide Sequence/ SEQ Leaf Rosette Line ID NO: Driver Target Photosynthesis Chlorophyll [N] RBP45A/ 42 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1940 Increased Increased No effect Line 1 (15%) (8%) (<1%) RBP45A/ 42 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1940 Increased Decreased — Line 2 (12%) (10%) RBP45A/ 42 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1940 Increased Increased Decreased Line 3 (11%) (4%) (3%) RBP45A/ 42 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1940 Increased Increased Decreased Line 4 (14%) (16%) (4%) RBP45A/ 42 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1940 Increased Decreased Decreased Line 5 (15%) (1%) (5%) RBP45A/ 42 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1940 Decreased Increased Increased Line 6 (3%) (11%) (1%)

The results presented in Table 24 were determined after screening six independent transgenic events. Photosynthetic rate and leaf chlorophyll were screened in two independent experiments for lines 1, and 3, and the effect size reported for is the mean of the two screening runs. The direction of the effect was the same in each screening run. Lines 2, 4, 5, and 6 were screened once. Rosette nitrogen data was collected in one experiment.

Table 25 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing TCP6 in experiments conducted to date. Table 25 describes increased photosynthesis in eight independent lines overexpressing TCP6. When averaged for these eight lines, photosynthetic rate was increased by 14% in the TCP6 overexpression lines. Leaf chlorophyll absorbs light energy utilized for photosynthesis, and was increased by 17% across the eight lines studied. Leaf chlorophyll and photosynthetic enzymes are a major sink for plant nitrogen. However, rosette nitrogen content increased by only 3% when averaged across the six lines for which data is available in Table 7. That photosynthesis and leaf chlorophyll content can be increased with negligible effects on rosette nitrogen content is evidence that TCP6 overexpression improves the efficiency with which photosynthesis operates relative to nitrogen availability.

All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a TCP6 related polypeptide or overexpress a TCP6 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.

TABLE 25 Components of increased photosynthetic resource use efficiency in TCP6 overexpression lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), leaf chlorophyll content and rosette nitrogen concentration (rosette [N]). Polypeptide Sequence/ SEQ Leaf Rosette Line ID NO: Driver Target Photosynthesis Chlorophyll [N] TCP6/ 86 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1936 Increased Increased Increased Line 1 (9%) (10%) (2%) TCP6/ 86 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1936 Increased Increased Increased Line 2 (14%) (15%) (4%) TCP6/ 86 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1936 Increased Increased Increased Line 3 (10%) (17%) (18%) TCP6/ 86 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1936 Increased Increased Decreased Line 4 (19%) (14%) (4%) TCP6/ 86 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1936 Increased Increased No effect Line 5 (20%) (10%) TCP6/ 86 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1936 Increased Increased Decreased Line 6 (17%) (24%) (4%) TCP6/ 86 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1936 Increased Increased — Line 7 (21%) (42%) TCP6/ 86 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1936 Increased Increased — Line 8 (3%) (6%)

The results presented in Table 25 were determined after screening eight independent transgenic events. Lines 1, 2 and 3 were screened in three independent experiments and the effect size reported for a given parameter is the mean of the three screening runs. Lines 4, 5, 6, 7 and 8 were screened once.

Table 26 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing PIL1 in experiments conducted to date. Table 26 describes increased photosynthesis in six independent lines overexpressing PILL When averaged for these six lines, photosynthetic rate was increased by 15% in the PIL1 overexpression lines. Leaf chlorophyll absorbs light energy utilized for photosynthesis, and was decreased by 2% across three lines for which data was collected. Rosette nitrogen content was increased by 1% in the same three lines. That photosynthesis could be increased in PIL1 overexpression lines while decreasing investment in chlorophyll and for a much smaller relative increase in nitrogen is evidence that PIL1 overexpression improves the efficiency with which photosynthesis operates relative to availability of the key resources of light and nitrogen.

All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a PIL1-related polypeptide or overexpress a PIL1 clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.

TABLE 26 Components of increased photosynthetic resource use efficiency in PIL1 overexpression lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), leaf chlorophyll content and rosette nitrogen concentration (rosette [N]). Polypeptide Sequence/ SEQ Leaf Rosette Line ID NO: Driver Target Photosynthesis Chlorophyll [N] PIL1/ 108 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1649 Increased Decreased Decreased Line 1 (17%) (2%) (3%) PIL1/ 108 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1649 Increased Decreased Decreased Line 2 (9%) (6%) (2%) PIL1/ 108 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1649 Increased Decreased Increased Line 3 (16%) (4%) (3%) PIL1/ 108 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1649 Increased — — Line 4 (23%) PIL1/ 108 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1649 Increased — — Line 5 (19%) PIL1/ 108 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1649 Increased — — Line 6 (18%)

The results presented in Table 26 were determined after screening six independent transgenic events. Photosynthetic rate was screened in two independent experiments for lines 1, and 2, and the effect size reported for is the mean of the two screening runs. The direction of the effect was the same in each screening run. Lines 3, 4, 5, and 6 were screened once.

Table 27 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing PCL1 in experiments conducted to date.

The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air, to sugars in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthesis and photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Table 27 describes increased photosynthesis in four out of five independent lines overexpressing PCL1. When averaged for these five lines photosynthetic rate was increased by 14% in the PCL1 overexpression lines. Table 27 also details how for four of these PCL1 overexpression lines this increase in photosynthetic rate is observed in lines that also displayed an increase in the capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the activity of Rubisco is a key constraint. FIG. 13 displays evidence of increased in both Rubisco activity in four out of five PCL1 overexpression lines (Long & Bernacchi 2003 already cited above, describe the basis for assaying Rubisco activity and RuBP regeneration capacity).

TABLE 27 Components of increased photosynthetic resource use efficiency in PCL1 overexpression lines. The effects and relative effect size is displayed for leaf photosynthetic rate (photosynthesis) Effects on photosynthetic capacity are also described and where known the biochemical basis for the effect is described as either due to effects on Rubisco activity (Rubisco) or the capacity to regenerate RuBP (RuBP). Polypeptide SEQ Sequence/ ID Photosynthetic Line NO: Driver Target Photosynthesis Capacity PCL1/ 126 35S::m355::oEnh:LexA: opLexA:: Increased Increased Line 1 GAL4_opLexA::GFP G2741 (16%) Rubisco PCL1/ 126 35S::m355::oEnh:LexA: opLexA:: Increased Increased Line 2 GAL4_opLexA::GFP G2741 (30%) Rubisco PCL1/ 126 35S::m355::oEnh:LexA: opLexA:: Increased Increased Line 3 GAL4_opLexA::GFP G2741 (9%) Rubisco PCL1/ 126 35S::m355::oEnh:LexA: opLexA:: Decreased No effect Line 4 GAL4_opLexA::GFP G2741 (3%) PCL1/ 126 35S::m355::oEnh:LexA: opLexA:: Increased Increased Line 5 GAL4_opLexA::GFP G2741 (17%) Rubisco

The results presented in Table 27 were determined after screening five independent transgenic events. Lines 1 and 2 were screened three times, lines 3, 4 and 5 were screened twice. For all lines the effect size shown is the mean of the individual effects recorded in each independent screening run.

Table 28 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing GTL1 in experiments conducted to date.

The ability of a crop canopy to photosynthesize, and the rate at which it can do this relative to the availability of resources, is an important determinant of crop yield. Consequently, increasing the rate of photosynthesis relative to resources that can limit productivity and yield is considered a pathway to improving crop yield across broad acres. Table 28 describes an increase in leaf photosynthetic rate in GTL1 overexpression lines for plants that had decreased leaf chlorophyll content and rosette nitrogen concentration. When averaged for the four lines studied, photosynthetic rate was increased by 12% and leaf chlorophyll content decreased by 20%. Rosette nitrogen content was decreased by 6%, when averaged over the three out of the four lines for which it was measured. Increasing photosynthesis while decreasing both chlorophyll and nitrogen in the rosette provides evidence that GTL1 overexpression improves the efficiency with which photosynthesis operates relative to availability of the key resources of light and nitrogen. This combination of phenotypes would be expected to increase light-limited photosynthesis in the crop canopy while providing protection against photodamage to the photosynthetic apparatus, associated with excess light absorption, in upper canopy leaves.

TABLE 28 Components of increased photosynthetic resource use efficiency in GTL1 overexpression lines. Effects and relative effect size are displayed for leaf chlorophyll content, photosynthetic rate (photosynthesis) and rosette nitrogen concentration (rosette [N]). Polypeptide Sequence/ SEQ Leaf Rosette Line ID NO: Driver Target Chlorophyll Photosynthesis [N] GTL1/ 156 prRBCS4::LexA:GAL4_opLexA::GFP, opLexA::G634 Decreased Increased Decreased Line 1 Col_Wt (18%) (10%) (7%) GTL1/ 156 prRBCS4::LexA:GAL4_opLexA::GFP, opLexA::G634 Decreased Decreased Decreased Line 2 Col_Wt (12%) (3%) (6%) GTL1/ 156 prRBCS4::LexA:GAL4_opLexA::GFP, opLexA::G634 Decreased Increased Decreased Line 3 Col_Wt (22%) (14%) (5%) GTL1/ 156 prRBCS4::LexA:GAL4_opLexA::GFP, opLexA::G634 Decreased Increased — Line 4 Col Wt (26%) (22%)

The results presented in Table 28 were determined after screening four independent transgenic events. Lines 1 and 3 were screened twice, and the effect shown is the mean of the effect observed in both experiments. Lines 2 and 4 were screened once.

Table 29 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing DREB2H in experiments conducted to date. Table 29 describes a decrease in leaf chlorophyll in G1755 overexpression lines that has no effect on photosynthetic rate. When averaged for the six lines studied, leaf chlorophyll content was decreased by 19%, while photosynthetic rate was increased by 2%.

Increasing photosynthesis while decreasing chlorophyll provides evidence that DREB2H overexpression improves the efficiency with which photosynthesis operates relative to light availability. This combination of phenotypes would be expected to increase light-limited photosynthesis in the crop canopy while providing protection against photodamage to the photosynthetic apparatus, associated with excess light absorption, in upper canopy leaves.

All experimental observations of greater photosynthetic resource use efficiency were made by comparison to control plants (e.g., plants that did not comprise a recombinant construct encoding a DREB2H-related polypeptide or overexpress a DREB2H clade or phylogenetically-related regulatory protein). Where a numerical value was determined, the percentage increases (+%) or decreases (−%) relative to control plants are shown in parentheses.

TABLE 29 Components of increased photosynthetic resource use efficiency in DREB2H overexpression lines. Effecbts and relative effect size are displayed for leaf chlorophyll content and photosynthetic rate(photosynthesis). SEQ Polypeptide ID Leaf Sequence/Line NO: Driver Target Chlorophyll Photosynthesis DREB2H/ 192 35S::m35S::oEnh: opLexA::G1755 Decreased Increased Line 1 LexA:GAL4_opLexA::GFP, Col_Wt (18%) (6%) DREB2H/ 192 35S::m35S::oEnh: opLexA::G1755 Decreased No effect Line 2 LexA:GAL4_opLexA::GFP, Col_Wt (19%) (<1%) DREB2H/ 192 355::m355::oEnh: opLexA::G1755 Decreased Decreased Line 3 LexA:GAL4_opLexA::GFP, Col_Wt (17%) (9%) DREB2H/ 192 355::m355::oEnh: opLexA::G1755 Decreased Decreased Line 4 LexA:GAL4_opLexA::GFP, Col_Wt (21%) (9%) DREB2H/ 192 355::m355::oEnh: opLexA::G1755 Decreased Increased Line 5 LexA:GAL4_opLexA::GFP, Col_Wt (14%) (32%) DREB2H/ 192 355::m355::oEnh: opLexA::G1755 Decreased Increased Line 6 LexA:GAL4_opLexA::GFP, Col_Wt (24%) (4%)

The results presented in Table 29 were determined after screening six independent transgenic events. Lines 2 and 3 were screened twice, and the effect shown is the mean of the effect observed in both experiments. Lines 1, 4, 5 and 6 were screened once.

FIGS. 20 and 21 detail indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing ERF087 in experiments conducted to date.

The ability of a crop canopy to photosynthesize, and the rate at which it can do this relative to the availability of resources, is an important determinant of crop yield. Consequently, increasing the rate of photosynthesis relative to resources that can limit productivity and yield is considered a pathway to improving crop yield across broad acres. FIGS. 20 and 21 show lower levels of non-photochemical quenching in five out of six ERF087 overexpression lines, as plants acclimated to a sudden increase in light incident on the leaves. The decrease in the ERF087 overexpression lines was most pronounced for plants acclimated to an air temperature of 35° C. (FIG. 21), but was also seen for measurements made at a growth temperature of 22° C. (FIG. 20). Non-photochemical quenching is a term that covers a range of processes that collectively dissipate absorbed light energy as heat from the light harvesting antenna, and thereby regulating the supply of light energy to photosystem two. Decreasing non-photochemical quenching would be expected to increase the efficiency of light energy transfer to the photosynthetic reaction centers and increase the light-use efficiency of photosynthesis.

Table 30 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing BBX18 in experiments conducted to date.

The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air, to sugars in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthesis and photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Table 30 describes increased photosynthesis in six out of six independent lines overexpressing BBX18. When averaged for these six lines photosynthetic rate was increased by 28% in the BBX18 overexpression lines. Table 30 also details how for all six of these BBX18 overexpression lines this increase in photosynthetic rate is observed in with an increase in the capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the activity of Rubisco and the capacity to regenerate RuBP, in the Calvin cycle are key constraints. FIG. 24 displays evidence of an increase in both Rubisco activity and the capacity to regenerate RuBP in the three of the six BBX18 overexpression lines that were assayed for insights into the biochemical basis for increased photosynthetic capacity (Long & Bernacchi 2003 already cited above, describe the basis for assaying Rubisco activity and RuBP regeneration capacity). When averaged over the six lines assayed, the increase in photosynthetic capacity and photosynthetic rate observed in the BBX18 overexpression lines was achieved with no increase in leaf chlorophyll content, providing evidence of optimization of resources within the photosynthetic apparatus.

TABLE 30 Components of increased photosynthetic resource use efficiency in BBX18 overexpression lines. The effects and relative effect size is displayed for leaf photosynthetic rate (photosynthesis) Effects on photosynthetic capacity are also described and, where known the biochemical basis for the effect is described as either due to effects on Rubisco activity (Rubisco) or the capacity to regenerate RuBP (RuBP). Polypeptide Chlorophyll Sequence/ SEQ Photosynthetic Content Line ID NO: Driver Target Photosynthesis Capacity Index BBX18/ 278 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1881 Increased Increased Decreased Line 1 (3%) (7%) BBX18/ 278 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1881 Increased Increased Decreased Line 2 (16%) (10%) BBX18/ 278 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1881 Increased Increased Decreased Line 3 (16%) (6%) BBX18/ 278 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1881 Increased Increased Increased Line 4 (30%) Rubisco/RuBP (8%) BBX18/ 278 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1881 Increased Increased Increased Line 5 (72%) Rubisco/RuBP (5%) BBX18/ 278 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1881 Increased Increased Increased Line 6 (30%) Rubisco/RuBP (10%)

Table 31 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing bHLH60 in experiments conducted to date. Table 31 describes a decrease in leaf chlorophyll in bHLH60 overexpression lines that has no effect on photosynthetic rate. When averaged for the six lines studied, leaf chlorophyll content was decreased by 15%, while photosynthetic rate was decreased by 7%.

Decreasing chlorophyll provides evidence that bHLH60 overexpression improves the efficiency with which photosynthesis operates relative to light availability. This combination of phenotypes would be expected to increase light-limited photosynthesis in the crop canopy while providing protection against photodamage to the photosynthetic apparatus, associated with excess light absorption, in upper canopy leaves.

TABLE 31 Components of increased photosynthetic resource use efficiency in bHLH60 overexpression lines. Effects and relative effect size are displayed for leaf chlorophyll content and photosynthetic rate (photosynthesis). SEQ Polypeptide NO: Leaf Sequence/Line ID Driver Target Chlorophyll Photosynthesis bHLH60/ 318 35S::m35S::oEnh:LexA:GA opLexA::G2144 Decreased Decreased Line 1 L4_opLexA::GFP, Col_Wt (16%) (8%) bHLH60/ 318 35S::m35S::oEnh:LexA:GA opLexA::G2144 Decreased Increased Line 2 L4_opLexA::GFP, Col_Wt (14%) (2%) bHLH60/ 318 35S::m35S::oEnh:LexA:GA opLexA::G2144 Decreased Decreased Line 3 L4_opLexA::GFP, Col_Wt (17%) (4%) bHLH60/ 318 35S::m35S::oEnh:LexA:GA opLexA::G2144 Decreased Decreased Line 4 L4_opLexA::GFP, Col_Wt (11%) (17%)

The results presented in Table 31 were determined after screening four independent transgenic events. Line 1 and 2 were screened twice and the data presented is the mean of the results of those two experiments. Lines 3 and 4 were screened once.

Table 32 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing NF-YC6 in experiments conducted to date. Table 32 describes a decrease in leaf chlorophyll in NF-YC6 overexpression lines that has no effect on photosynthetic rate. When averaged for the five lines studied, leaf chlorophyll content was decreased by 13%, while photosynthetic rate was unaffected (<1% change). Rosette nitrogen content was measured for three of the five lines studied. Averaged for these three lines, rosette nitrogen content was decreased by 7% from 7.3 to 6.7% of rosette dry weight. Increasing photosynthesis while decreasing both chlorophyll and nitrogen in the rosette provides evidence that NF-YC6 overexpression improves the efficiency with which photosynthesis operates relative to the availability of the key resources of light and nitrogen. This combination of phenotypes would be expected to increase light-limited photosynthesis in the crop canopy while providing protection against photodamage to the photosynthetic apparatus, associated with excess light absorption, in upper canopy leaves.

TABLE 32 Components of increased photosynthetic resource use efficiency in NF-YC6 overexpression lines. Effects and relative effect size are displayed for leaf chlorophyll content, photosynthetic rate (photosynthesis) and rosette nitrogen concentration (rosette [N]). Polypeptide Sequence/ SEQ Leaf Rosette Line ID NO: Driver Target Chlorophyll Photosynthesis [N] NF-YC6/ 356 35S::m35S::oEnh:LexA:GAL4_opLexA:: GFP, opLexA::G1820 Decreased Decreased Decreased Line 1 Col_Wt (12%) (2%) (2%) NF-YC6/ 356 35S::m35S::oEnh:LexA:GAL4_opLexA:: GFP, opLexA::G1820 Decreased Increased Decreased Line 2 Col_Wt (17%) (8%) (9%) NF-YC6/ 356 35S::m35S::oEnh:LexA:GAL4_opLexA:: GFP, opLexA::G1820 Decreased Decreased Decreased Line 3 Col_Wt (11%) (3%) (11%) NF-YC6/ 356 35S::m35S::oEnh:LexA:GAL4_opLexA:: GFP, opLexA::G1820 Decreased No effect Line 4 Col_Wt (20%) (<1%) NF-YC6/ 356 35S::m35S::oEnh:LexA:GAL4_opLexA:: GFP, opLexA::G1820 Decreased No effect Line 5 Col_Wt (4%) (<1%)

The results presented in Table 32 were determined after screening five independent transgenic events. Lines 1, 2 and 3 were screened twice and the effect size reported for a given parameter is the mean of the two screening runs. Lines 4 and 5 were screened once.

Table 33 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing bHLH121 in experiments conducted to date.

The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air, to sugars in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthesis and photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Table 33 describes increased photosynthesis in five out of five independent lines overexpressing bHLH121. When averaged for these five bHLH121 overexpression lines, photosynthetic rate was increased by 11%. Table 33 also details how for four of the five lines, the increase in photosynthetic rate is linked to an increase in capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the capacity to regenerate RuBP in the Calvin cycle is a key constraint. FIG. 31 displays evidence of an increase in the capacity to regenerate RuBP in four of the five bHLH121 overexpression lines (Long & Bernacchi 2003 already cited above, describe the basis for RuBP regeneration capacity). All the bHLH121 lines screened were grown in the same environment as the control lines, consequently the increase in photosynthetic capacity and photosynthetic rate observed has been achieved through an increase in photosynthetic resource-use efficiency in these lines.

TABLE 33 Components of increased photosynthetic resource use efficiency in bHLH121 overexpression lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), photosynthetic capacity and leaf chlorophyll content. Where known, the biochemical basis for increase in photosynthetic capacity is described as either due to effects on Rubisco activity (Rubisco) or the capacity to regenerate RuBP (RuBP). Polypeptide Leaf Sequence/ SEQ Photosynthetic Chlorophyll Line ID NO: Driver Target Photosynthesis capacity content bHLH121/ 388 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G782 Increased Increased Increased Line 1 (18%) RuBP (21%) bHLH121/ 388 35S::m35S:oEnh:LexA:GAL4_opLexA:: GFP opLexA::G782 Increased No effect Increased Line 2 (12%) (18%) bHLH121/ 388 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G782 Increased Increased Increased Line 3 (8%) RuBP (8%) bHLH121/ 388 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G782 Increased Increased Increased Line 4 (2%) RuBP (9%) bHLH121/ 388 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G782 Increased Increased Increased Line 5 (14%) RuBP (21%)

The results presented in Table 33 were determined after screening six independent transgenic events. Lines 1 and 2 were screened twice and the effect size reported for a given parameter is the mean of the two screening runs. For both lines the direction of the effect was the same in both runs. Lines 3, 4 and 5 were screened once.

Table 34 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing BBX26 in experiments conducted to date. Table 34 describes increased photosynthesis in five out of five independent lines overexpressing BBX26 When averaged for these five BBX26 overexpression lines, photosynthetic rate was increased by 14%. Table 34 also details how for all five lines, the increase in photosynthetic rate is linked to an increase in capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the capacity to regenerate RuBP in the Calvin cycle is a key constraint. FIG. 34 displays evidence of an increase in the capacity to regenerate RuBP in four of the five BBX26 overexpression lines (Long & Bernacchi 2003 already cited above, describe the basis for RuBP regeneration capacity). Photosynthetic resource use efficiency was also increased in lines overexpressing BBX26. When averaged for these five lines, the 14% increase in photosynthetic rate was observed in tandem with a 13% increase in leaf chlorophyll content, but also with an 8% decrease in rosette nitrogen content from 7.0% to 6.4%, evidence that leaf nitrogen was being preferentially apportioned to the photosynthetic apparatus.

TABLE 34 Components of increased photosynthetic resource use efficiency in BBX26 overexpression lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), leaf chlorophyll content and rosette nitrogen concentration (rosette [N]). Effects on photosynthetic capacity (P. Cap) are also described and where known, the biochemical basis for the effect is described as either due to effects on Rubisco activity (Rubisco) or the capacity to regenerate RuBP (RuBP). Polypeptide Leaf Sequence/ SEQ Chlorophyll Rosette Line ID NO: Driver Target Photosynthesis P. Cap content [N] BBX26/ 410 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1486 Increased Increased Increased Decreased Line 1 (15%) RuBP (9%) (6%) BBX26/ 410 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1486 Increased Increased Increased Decreased Line 2 (13%) (24%) (5%) BBX26/ 410 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1486 Increased Increased Increased Decreased Line 3 (17%) RuBP (20%) (4%) BBX26/ 410 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1486 Increased Increased Increased Decreased Line 4 (15%) RuBP (23%) (2%) BBX26/ 410 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G1486 Increased Increased Decreased Decreased Line 5 (10%) RuBP (10%) (2%)

The results presented in Table 34 were determined after screening six independent transgenic events. Lines 1 and 2 were screened twice and the effect size reported for a given parameter is the mean of the two screening runs. For both lines the direction of the effect was the same in both runs. Lines 3, 4, 5 and 6 were screened once.

Table 35 details indicators of photosynthetic resource use efficiency observed in Arabidopsis plants overexpressing PMT24 in experiments conducted to date.

The biochemical capacity for photosynthesis is a key determinant of the efficiency with which photosynthesis operates relative to resources required for plant growth. The biochemical capacity for photosynthesis is the product of plant resource investment in numerous pigments and proteins required to absorb light and couple it to the enzymatic reduction of carbon in the air, to sugars in the chloroplast. This capacity for photosynthesis sets limits upon the rate of photosynthesis that can be achieved by a leaf, and ultimately the yield potential of crops. Consequently, increasing photosynthesis and photosynthetic capacity is considered a pathway to improving crop yield across broad acres. Table 35 describes increased photosynthesis in five out of seven independent lines overexpressing PMT24. When averaged for these seven PMT24 overexpression lines, photosynthetic rate was increased by 18%. Table 35 also details how for five out of seven lines, the increase in photosynthetic rate is linked to an increase in capacity for photosynthesis. Of the numerous steps that can limit photosynthesis, the capacity to regenerate RuBP in the Calvin cycle is a key constraint. FIG. 34 displays evidence of an increase in the capacity to regenerate RuBP in four of the five PMT24 overexpression lines run through a focused secondary screen (Long & Bernacchi 2003 already cited above, describe the basis for RuBP regeneration capacity). This increase in photosynthetic capacity was achieved without any increase in leaf chlorophyll content, which was increased by less than 1% when averaged across all seven lines. These findings suggest that PMT24 overexpression changes resource investment in different components of the photosynthetic apparatus and, because all the PMT24 lines screened were grown in the same environment as the control lines, that the increase in photosynthetic capacity and photosynthetic rate observed has been achieved through an increase in photosynthetic resource-use efficiency in these lines.

TABLE 35 Components of increased photosynthetic resource use efficiency in PMT24 overexpression lines. Effects and relative effect size are displayed for leaf photosynthetic rate (photosynthesis), photosynthetic capacity and leaf chlorophyll content. Where know the biochemical basis for increase in photosynthetic capacity is described as either due to effects on Rubisco activity (Rubisco) or the capacity to regenerate RuBP (RuBP). Polypeptide Leaf Sequence/ SEQ Photosynthetic chlorophyll Line ID NO: Driver Target Photosynthesis capacity content PMT24/ 444 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G837 Increased Increased Decreased Line 1 (46%) (3%) PMT24/ 444 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G837 Increased No effect Increased Line 2 (26%) (2%) PMT24/ 444 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G837 Increased Increased Increased Line 3 (34%) RuBP (2%) PMT24/ 444 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G837 No effect Increased Increased Line 4 (<1%) RuBP (4%) PMT24/ 444 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G837 Decreased Increased No effect Line 5 (6%) RuBP (<1%) PMT24/ 444 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G837 Increased Increased Decreased Line 6 (14%) RuBP (4%) PMT24/ 444 35S::m35S::oEnh:LexA:GAL4_opLexA::GFP opLexA::G837 Increased No effect Increased Line 7 (11%) (3%)

The results presented in Table 35 were determined after screening seven independent transgenic events. Line 3 was screened twice and the effect size reported for a given parameter is the mean of the two screening runs. All other lines were screened once.

The present disclosure thus describes how the transformation of plants, which may include monocots and/or dicots, with an AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide can confer to the transformed plants greater photosynthetic resource use efficiency than the level of photosynthetic resource use efficiency exhibited by control plants. In one embodiment, expression of AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 is driven by a constitutive promoter. In another embodiment, expression of AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 is driven by a promoter with enhanced activity in a tissue capable of photosynthesis (also referred to herein as a “photosynthetic promoter” or a “photosynthetic tissue-enhanced promoter”) such as a leaf tissue or other green tissue. Examples of photosynthetic tissue-enhanced promoters include for example, an RBCS3 promoter (SEQ ID NO: 862), an RBCS4 promoter (SEQ ID NO: 863) or others such as the At4g01060 (also referred to as “G682”) promoter (SEQ ID NO: 864), the latter regulating expression in guard cells, or promoters listed in Table 4. Other photosynthetic tissue-enhanced promoters have been taught by Bassett et al., 2007. BMC Biotechnol. 7: 47, specifically incorporated herein by reference in its entirety. Other photosynthetic tissue-enhanced promoters of interest include those from the maize aldolase gene FDA (U.S. patent publication no. 20040216189, specifically incorporated herein by reference in its entirety), and the aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al., 2000. Plant Cell Physiol. 41:42-48, specifically incorporated herein by reference in its entirety). Other tissue enhanced promoters or inducible promoters are also envisioned that may be used to regulate expression of the disclosed clade member polypeptides and improve photosynthetic resource use efficiency in a variety of plants.

Example VI. Utilities of AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 Clade Sequences for Improving Photosynthetic Resource Use Efficiency, Yield or Biomass

By expressing the present polynucleotide sequences in a commercially valuable plant, the plant's phenotype may be altered to one with improved traits related to photosynthetic resource use efficiency or yield. The sequences may be introduced into the commercially valuable plant, by, for example, introducing the polynucleotide in an expression vector or cassette to produce a transgenic plant, or by crossing a target plant with a second plant that comprises said polynucleotide. The transgenic or target plant may be any valuable species of interest, including but not limited to a crop or model plant such as a wheat, Setaria, corn (maize), rice, barley, rye, millet, sorghum, turfgrass, sugarcane, miscane, turfgrass, Miscanthus, switchgrass, soybean, cotton, rape, oilseed rape including canola, Eucalyptus, or poplar plant. The present polynucleotide sequences encode an AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide sequence and the ectopic expression or overexpression in the transgenic or target plant of any of said polypeptides, for example, a polypeptide comprising any of SEQ ID NOs: 2, 42, 86, 108, 126, 156, 192, 246, 278, 318, 356, 388, 410, 444, or SEQ ID NOs: 2n where n=1 to 241, or at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to any of SEQ ID NOs: 2, 42, 86, 108, 126, 156, 192, 246, 278, 318, 356, 388, 410, or 444, and/or SEQ ID NOs: 2n, where n=1 to 241, and/or at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100% amino acid identity to a domain of any of SEQ ID NOs: 483, 490, 510, 538, 566, 588, 599, 608, 623, 629, 659, 686, 702, 721, 741, 760, 769, 786, 813, and/or at least 90%, 91%, 92%, 93%, 94%, 95% m 96% m 97%, 98%, 99%, or about 100% identity to any of consensus sequences SEQ ID NOs: 842-861, can confer improved photosynthetic resource use efficiency or yield in the plant. For plants for which biomass is the product of interest, increasing the expression level of AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade of polypeptide sequences may increase yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant of the plants. Thus, it is thus expected that these sequences will improve yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant in non-Arabidopsis plants relative to control plants. This yield improvement may result in yield increases of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30% or greater yield relative to the yield that may be obtained with control plants.

It is expected that the same methods may be applied to identify other useful and valuable sequences that are functionally-related and/or closely-related to the listed sequences or domains provided in the instant Tables, and the sequences may be derived from diverse species. Because of morphological, physiological and photosynthetic resource use efficiency similarities that may occur among closely-related sequences, the disclosed clade sequences are expected to increase yield, light use efficiency, photosynthetic capacity, photosynthetic rate, photosynthetic resource use efficiency, vigor, and/or biomass as compared to a control plant to a variety of crop plants, ornamental plants, and woody plants used in the food, ornamental, paper, pulp, lumber or other industries.

Example VII: Expression and Analysis of Increased Yield or Photosynthetic Resource Use Efficiency in Non-Arabidopsis or Crop Species

Northern blot analysis, RT-PCR or microarray analysis of the regenerated, transformed plants may be used to show expression of a polypeptide or the instant description and related genes that are capable of inducing improved photosynthetic resource use efficiency, and/or larger size.

After a eudicot plant, monocot plant or plant cell has been transformed (and the latter plant host cell regenerated into a plant) and shown to have or produce increased yield, increased light use efficiency, increased photosynthetic capacity, increased photosynthetic rate, photosynthetic resource use efficiency, greater vigor, and/or greater biomass as compared to a control plant relative to a control plant, the transformed monocot plant may be crossed with itself or a plant from the same line, a non-transformed or wild-type monocot plant, or another transformed monocot plant from a different transgenic line of plants.

The function of one or more specific polypeptides of the instant description has been analyzed and may be further characterized and incorporated into crop plants. The ectopic overexpression of one or more of the disclosed clade polypeptide sequences may be regulated using constitutive, inducible, or tissue-enhanced regulatory elements. Genes that have been examined have been shown to modify plant traits including increasing yield and/or photosynthetic resource use efficiency. It is expected that newly discovered polynucleotide and polypeptide sequences closely related, as determined by the disclosed hybridization or identity analyses, to polynucleotide and polypeptide sequences found in the Sequence Listing can also confer alteration of traits in a similar manner to the sequences found in the Sequence Listing, when transformed into any of a considerable variety of plants of different species, and including dicots and monocots. The polynucleotide and polypeptide sequences derived from monocots (e.g., the rice sequences) may be used to transform both monocot and dicot plants, and those derived from dicots (e.g., the Arabidopsis and soy genes) may be used to transform either group, although it is expected that some of these sequences will function best if the gene is transformed into a plant from the same group as that from which the sequence is derived.

As an example of a first step to determine photosynthetic resource use efficiency, seeds of these transgenic plants may be grown as described above or methods known in the art.

Closely-related homologs of AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 derived from various diverse plant species may be overexpressed in plants and have the same functions of conferring increased photosynthetic resource use efficiency. It is thus expected that structurally similar orthologs of the disclosed polypeptide clades, including SEQ ID NOs: 2n where n=1 to 241, orthologs that comprise any of consensus sequences SEQ ID NOs: 842-861, can confer increased yield, increased light use efficiency, increased photosynthetic capacity, increased photosynthetic rate, increased photosynthetic resource use efficiency, greater vigor, greater biomass, and/or size, relative to control plants. As at least one sequence of the instant description has increased photosynthetic resource use efficiency in Arabidopsis, it is expected that the sequences provided in the Sequence Listing, or polypeptide sequences comprising one of or any of the conserved domains provided in the instant Tables, will increase the photosynthetic resource use efficiency and/or yield of transgenic plants including transgenic non-Arabidopsis (plant species other than Arabidopsis species) crop or other commercially important plant species, including, but not limited to, non-Arabidopsis plants and plant species such as monocots and dicots, wheat, Setaria, corn (maize), teosinte (Zea species which is related to maize), rice, barley, rye, millet, sorghum, turfgrass, sugarcane, miscane, turfgrass, Miscanthus, switchgrass, soybean, cotton, rape, oilseed rape including canola, tobacco, tomato, tomatillo, potato, sunflower, alfalfa, clover, banana, blackberry, blueberry, strawberry, raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, pumpkin, spinach, squash, sweet corn, watermelon, rosaceous fruits including apple, peach, pear, cherry and plum, and brassicas including broccoli, cabbage, cauliflower, Brussels sprouts, and kohlrabi, currant, avocado, citrus fruits including oranges, lemons, grapefruit and tangerines, artichoke, cherries, endive, leek, roots such as arrowroot, beet, cassava, turnip, radish, yam, and sweet potato, beans, woody species including pine, poplar, Eucalyptus, mint or other labiates, nuts such as walnut and peanut. Within each of these species the closely-related homologs of AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 may be overexpressed or ectopically expressed in different varieties, cultivars, or germplasm.

The instantly disclosed transgenic plants comprising the disclosed recombinant polynucleotides can be enhanced with other polynucleotides, resulting in a plant or plants with “stacked” or jointly introduced traits, for example, the traits of increased photosynthetic resource use efficiency and improved yield combined with an enhanced trait resulting from expression of a polynucleotide that confers herbicide, insect or and/or pest resistance in a single plant or in two or more parental lines. The disclosed polynucleotides may thus be stacked with a nucleic acid sequence providing other useful or valuable traits such as a nucleic acid sequence from Bacillus thuringensis that confers resistance to hemiopteran, homopteran, lepidopteran, coliopteran or other insects or pests.

Thus, the disclosed sequences and closely related, functionally related sequences may be identified that, when ectopically expressed or overexpressed in plants, confer one or more characteristics that lead to greater photosynthetic resource use efficiency. These characteristics include, but are not limited to, the embodiments listed below.

1. A dicot or monocot transgenic plant that has greater or increased photosynthetic resource use efficiency^(†) relative to a control plant;

wherein the transgenic plant comprises an exogenous recombinant polynucleotide comprising a promoter selected from the group consisting of:

a constitutive promoter, a non-constitutive promoter, an inducible promoter, a tissue-enhanced promoter, and a photosynthetic tissue-enhanced promoter;

wherein the promoter regulates expression of a polypeptide having a percentage identity to an amino acid sequence comprising an AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide in a photosynthetic or green tissue of the transgenic plant;

wherein the percentage identity is at least:

-   -   26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%,         39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%,         52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%,         65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%,         78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,         91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100%         identity to the entire length of any of SEQ ID NOs: 2n, where         n=1-241; and/or     -   at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%,         39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%,         52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%,         65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%,         78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,         91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100%         identity to a domain of any of SEQ ID NOs: 483 to 841; and/or     -   at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%,         88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or         about 100% identical to a consensus sequence of any of SEQ ID         NO: 842-861; and/or     -   the exogenous recombinant polynucleotide hybridizes with any of         SEQ ID NO: 1, 41, 85, 107, 125, 155, 191, 245, 277, 317, 355,         387, 409, or 443 under stringent hybridization conditions         followed by one, two, or more wash steps of 6×SSC and 65° C. for         ten to thirty minutes per step;

wherein expression of the polypeptide under the regulatory control of the promoter confers greater or increased photosynthetic resource use efficiency in the transgenic plant relative to the control plant;

wherein the control plant does not comprise the recombinant polynucleotide; and/or

2. The transgenic plant of embodiment 1, wherein the photosynthetic tissue-enhanced promoter is an RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an Os02g09720 promoter, an Os05g34510 promoter, an Os11g08230 promoter, an Os01g64390 promoter, an Os06g15760 promoter, an Os12g37560 promoter, an Os03g17420 promoter, an Os04g51000 promoter, an Os01g01960 promoter, an Os05g04990 promoter, an Os02g44970 promoter, an Os01g25530 promoter, an Os03g30650 promoter, an Os01g64910 promoter, an Os07g26810 promoter, an Os07g26820 promoter, an Os09g11220 promoter, an Os04g21800 promoter, an Os10g23840 promoter, an Os08g13850 promoter, an Os12g42980 promoter, an Os03g29280 promoter, an Os03g20650 promoter, or an Os06g43920 promoter (SEQ ID NO: 862-888, respectively), or a functional variant thereof, or a functional fragment thereof, or a promoter sequence that is at least 80% identical to SEQ ID NO: 862-888; and/or 3. The transgenic plant of embodiments 1 or 2, wherein:

the recombinant polynucleotide encodes the polypeptide which comprises any of SEQ ID NOs: 2n, where n=1-241; and/or

any of SEQ ID NOs: 483, 490, 510, 538, 566, 588, 599, 608, 623, 629, 659, 686, 702, 721, 741, 760, 769, 786, 813; and/or

any of SEQ ID NO: 842-861; and/or

4. The transgenic plant of any of embodiments 1 to 3, wherein the polypeptide is encoded by

(a) the exogenous recombinant polynucleotide, or

(b) a second exogenous recombinant polynucleotide and expression of the polypeptide is regulated by a trans-regulatory element; and/or

5. The transgenic plant of any of embodiments 1 to 4, wherein a plurality of the transgenic plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density; and/or 6. The transgenic plant of any of embodiments 1 to 5, wherein the transgenic plant produces a greater yield than the control plant, including, but not limited to, a greater yield of: vegetative biomass, plant parts, whole plants, shoot vegetative organs/structures (for example, leaves, stems and tubers), roots, flowers and floral organs/structures (for example, bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (for example, vascular tissue, ground tissue, pulped, pureed, ground-up, macerated or broken-up tissue, and the like) and cells (for example, guard cells, egg cells, and the like); and/or 7. The transgenic plant of any of embodiments 1 to 6, wherein the transgenic plant is selected from the group consisting of a corn, wheat, rice, Setaria, Miscanthus, switchgrass, ryegrass, sugarcane, miscane, barley, sorghum, turfgrass, soy, cotton, canola, rapeseed, Crambe, Camelina, sugar beet, alfalfa, tomato, Eucalyptus, poplar, willow, pine, birch and a woody plant; and/or 8. The transgenic plant of any of embodiments 1 to 7, wherein the transgenic plant is morphologically similar to the control plant at one or more stages of growth, and/or developmentally similar to the control plant. 9. A method for increasing photosynthetic resource use efficiency^(t) in a dicot or monocot plant, the method comprising:

(a) providing one or more dicot or monocot plants that comprise an exogenous recombinant polynucleotide comprising a promoter selected from the group consisting of:

a constitutive promoter, a non-constitutive promoter, an inducible promoter, a tissue-enhanced promoter, and a photosynthetic tissue-enhanced promoter;

wherein the promoter regulates expression of a polypeptide having a percentage identity to an amino acid sequence comprising an AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide in a photosynthetic or green tissue of the dicot or monocot plant;

wherein the percentage identity is at least:

-   -   26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%,         39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%,         52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%,         65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%,         78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,         91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100%         identity to the entire length of any of SEQ ID NOs: 2n, where         n=1-241; and/or     -   at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%,         39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%,         52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%,         65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%,         78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,         91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or about 100%         identity to a domain of any of SEQ ID NOs: 483 to 841; and/or     -   at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%,         88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%, 98%, 99%, or         about 100% identical to a consensus sequence of any of SEQ ID         NO: 842-861; and/or     -   the exogenous recombinant polynucleotide hybridizes with any of         SEQ ID NO: 1, 41, 85, 107, 125, 155, 191, 245, 277, 317, 355,         387, 409, or 443 under stringent hybridization conditions         followed by one, two, or more wash steps of 6×SSC and 65° C. for         ten to thirty minutes per step;     -   wherein expression of the polypeptide in the one or more dicot         or monocot plants confers greater or increased photosynthetic         resource use efficiency relative to a control plant that does         not comprise the recombinant polynucleotide; and

(b) growing the one or more dicot or monocot plants; and/or

10. The method of embodiment 9, wherein the photosynthetic tissue-enhanced promoter is an RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an Os02g09720 promoter, an Os05g34510 promoter, an Os11g08230 promoter, an Os01g64390 promoter, an Os06g15760 promoter, an Os12g37560 promoter, an Os03g17420 promoter, an Os04g51000 promoter, an Os01g01960 promoter, an Os05g04990 promoter, an Os02g44970 promoter, an Os01g25530 promoter, an Os03g30650 promoter, an Os01g64910 promoter, an Os07g26810 promoter, an Os07g26820 promoter, an Os09g11220 promoter, an Os04g21800 promoter, an Os10g23840 promoter, an Os08g13850 promoter, an Os12g42980 promoter, an Os03g29280 promoter, an Os03g20650 promoter, or an Os06g43920 promoter (SEQ ID NO: 862-888, respectively), or a functional variant thereof, or a functional fragment thereof, or a promoter sequence that is at least 80% identical to SEQ ID NO: 862-888; and/or 11. The method of embodiments 9 or 10, wherein an expression cassette comprising the recombinant polynucleotide is introduced into a target plant to produce the dicot or monocot plant comprising the exogenous recombinant polynucleotide; and/or 12. The method of any of embodiments 9 to 11, wherein the polypeptide is encoded by

(a) the exogenous recombinant polynucleotide, or

(b) a second exogenous recombinant polynucleotide and expression of the polypeptide is regulated by a trans-regulatory element; and/or

13. The method of any of embodiments 9 to 12, wherein the dicot or monocot plant is selected for having the increased photosynthetic resource use efficiency relative to the control plant; and/or

14. The method of any of embodiments 9 to 13, wherein the dicot or monocot plant produces a greater yield relative to the control plant; and/or

15. The method of any of embodiments 9 to 14, wherein the dicot or monocot plant is selected for having the greater yield relative to the control plant; and/or

16. The method of any of embodiments 9 to 15, wherein a plurality of the dicot or monocot plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density; and/or 17. The method of any of embodiments 9 to 16, wherein the dicot or monocot plant is selected from the group consisting of a corn, wheat, rice, Setaria, Miscanthus, switchgrass, ryegrass, sugarcane, miscane, barley, sorghum, turfgrass, soy, cotton, canola, rapeseed, Crambe, Camelina, sugar beet, alfalfa, tomato, Eucalyptus, poplar, willow, pine, birch and a woody plant; and/or 18. The method of any of embodiments 9 to 17, the method steps further including:

crossing the dicot or monocot plant with itself, a second plant from the same line as the dicot or monocot plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed.

19. A method for producing and selecting a dicot or monocot crop plant with greater yield or greater photosynthetic resource use efficiency^(†) than a control plant, the method comprising:

-   -   (a) providing one or more dicot or monocot transgenic plants         that comprise an exogenous recombinant polynucleotide comprising         a promoter selected from the group consisting of:         -   a constitutive promoter, a non-constitutive promoter, an             inducible promoter, a tissue-enhanced promoter, and a             photosynthetic tissue-enhanced promoter;         -   wherein the promoter regulates expression of a polypeptide             having a percentage identity to an amino acid sequence             comprising an AtMYB27, RBP45A, TCP6, PILL PCL1, GTL1,             DREB2H, ERF087, NF-YC6, BBX18, bHLH60, BBX26, bHLH121, or             PMT24 clade polypeptide in a photosynthetic or green tissue             of the dicot or monocot transgenic plant;         -   wherein the percentage identity is:         -   at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%,             36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%,             48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%,             60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%,             72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%,             84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%             or 96%, 97%, 98%, 99%, or about 100% identity to the entire             length of any of SEQ ID NOs: 2n, where n=1-241; and/or         -   at least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%,             38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%,             50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%,             62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%,             74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%,             86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%,             97%, 98%, 99%, or about 100% identity to a domain of any of             SEQ ID NOs: 483 to 841; and/or         -   at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%,             87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%,             98%, 99%, or about 100% identical to a consensus sequence of             any of SEQ ID NO: 842-861; and/or     -   the exogenous recombinant polynucleotide hybridizes with any of         SEQ ID NO: 1, 41, 85, 107, 125, 155, 191, 245, 277, 317, 355,         387, 409, or 443 under stringent hybridization conditions         followed by one, two, or more wash steps of 6×SSC and 65° C. for         ten to thirty minutes per step;         -   wherein the photosynthetic tissue-enhanced promoter does not             regulate protein expression in a constitutive manner;     -   (b) growing a plurality of the dicot or monocot transgenic         plants; and     -   (c) selecting a dicot or monocot transgenic plant that:         -   has greater photosynthetic resource use efficiency than the             control plant, wherein the control plant does not comprise             the recombinant polynucleotide; and/or         -   comprises the recombinant polynucleotide;     -   wherein expression of the polypeptide in the selected dicot or         monocot transgenic plant confers the greater photosynthetic         resource use efficiency or the greater yield relative to the         control plant; and/or         20. The method of embodiment 19, the method steps further         including:     -   (d) crossing the selected dicot or monocot transgenic plant with         itself, a second plant from the same line as the selected         transgenic plant, a non-transgenic plant, a wild-type plant, or         a transgenic plant from a different line of plants, to produce a         transgenic seed; and/or         21. The method of embodiment 19 or 20, wherein the dicot or         monocot transgenic plant is selected for having the increased         photosynthetic resource use efficiency relative to the control         plant; and/or         22. The method of any of embodiments 19 to 21, wherein a         plurality of the selected dicot or monocot transgenic plants         have greater cumulative canopy photosynthesis than the canopy         photosynthesis of the same number of the control plants grown         under the same conditions and at the same density; and/or         23. The method of any of embodiments 19 to 22, wherein the         selected dicot or monocot transgenic plant has an altered trait         that confers the greater photosynthetic resource use efficiency.         24. A method for producing a dicot or monocot crop plant with         greater photosynthetic resource use efficiency^(†) than a         control plant, the method comprising:     -   (a) providing a dicot or monocot transgenic plant that comprises         an exogenous recombinant polynucleotide that comprises a         promoter selected from the group consisting of:         -   a constitutive promoter, a non-constitutive promoter, an             inducible promoter, a tissue-enhanced promoter, or a             photosynthetic tissue-enhanced promoter;         -   wherein the promoter regulates expression of a polypeptide             comprising SEQ ID NO: 2, 42, 86, 108, 126, 156, 192, 246,             278, 318, 356, 388, 410, or 444 in a photosynthetic or green             tissue of the transgenic plant to a level that is effective             in conferring greater photosynthetic resource use efficiency             in the transgenic plant relative to the control plant; and     -   (b) measuring an altered trait that confers the greater         photosynthetic resource use efficiency,         -   wherein expression of the polypeptide in the selected dicot             or monocot transgenic plant confers the greater             photosynthetic resource use efficiency of the transgenic             plant relative to the control plant, thereby producing the             crop plant with greater photosynthetic resource use             efficiency than the control plant; and/or             25. The method of embodiment 24, wherein the transgenic             dicot or monocot plant is selected for having the increased             photosynthetic resource use efficiency relative to the             control plant.             26. A method for producing a monocot plant with increased             grain yield, said method including:     -   (a) providing a monocot plant cell or plant tissue with stably         integrated, exogenous recombinant polynucleotide comprising a         promoter (for example, a constitutive, a non-constitutive, an         inducible, a tissue-enhanced, or a photosynthetic         tissue-enhanced promoter) that is functional in plant cells and         that is operably linked to an exogenous or an endogenous nucleic         acid sequence that encodes a polypeptide that has a percentage         identity to an amino acid sequence comprising an AtMYB27,         RBP45A, TCP6, PIL1, PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18,         bHLH60, BBX26, bHLH121, or PMT24 clade polypeptide, wherein the         percentage identity is:         -   at least 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%,             36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%,             48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%,             60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%,             72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%,             84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%             or 96%, 97%, 98%, 99%, or about 100% identity to the entire             length of any of SEQ ID NOs: 2n, where n=1-241; and/or at             least 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%,             39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%,             51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%,             63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%,             75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%,             87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%,             98%, 99%, or about 100% identity to a domain of any of SEQ             ID NOs: 483 to 841; and/or         -   at least 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%,             87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95% or 96%, 97%,             98%, 99%, or about 100% identical to a consensus sequence of             any of SEQ ID NO: 842-861; and/or         -   the exogenous recombinant polynucleotide hybridizes with any             of SEQ ID NO: 1, 41, 85, 107, 125, 155, 191, 245, 277, 317,             355, 387, 409, or 443 under stringent hybridization             conditions followed by one, two, or more wash steps of 6×SSC             and 65° C. for ten to thirty minutes per step;     -   (b) generating a monocot plant from the plant cell or the plant         tissue, wherein the monocot plant comprises the exogenous         recombinant polynucleotide, wherein the polypeptide is expressed         in a photosynthetic or green tissue of the monocot plant to a         level that is effective in conferring greater photosynthetic         resource use efficiency† in the monocot plant relative to a         control plant that does not contain the recombinant         polynucleotide;     -   (c) growing the monocot plant; and     -   (d) measuring an increase in photosynthetic resource use         efficiency of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%,         11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%,         24%, 25%, 26%, 2%, 28%, 29%, or 30% relative to the control         plant, or an increase in grain yield of at least 1%, 2%, 3%, 4%,         5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%,         19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 2%, 28%, 29%, or 30% or         at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,         17, 18, 19, 20 bushels per acre;     -   thereby producing the monocot plant with increased grain yield         relative to the control plant; and/or         27. The method of embodiment 26, wherein the AtMYB27, RBP45A,         TCP6, PILL PCL1, GTL1, DREB2H, ERF087, NF-YC6, BBX18, bHLH60,         BBX26, bHLH121, or PMT24 clade polypeptide comprises a consensus         sequence of one or more of any of SEQ ID NOs: 842-861; and/or         28. A transgenic monocot plant produced by the method of         embodiment 26; and/or         29. The transgenic monocot plant of embodiment 28, wherein         transgenic monocot plant is a corn, wheat, rice, Miscanthus,         Setaria, switchgrass, ryegrass, sugarcane, miscane, barley,         sorghum or turfgrass plant; and/or         30. The method of embodiment 26, wherein the promoter is an         RBCS3 promoter, an RBCS4 promoter, an At4g01060 promoter, an         Os02g09720 promoter, an Os05g34510 promoter, an Os11g08230         promoter, an Os01g64390 promoter, an Os06g15760 promoter, an         Os12g37560 promoter, an Os03g17420 promoter, an Os04g51000         promoter, an Os01g01960 promoter, an Os05g04990 promoter, an         Os02g44970 promoter, an Os01g25530 promoter, an Os03g30650         promoter, an Os01g64910 promoter, an Os07g26810 promoter, an         Os07g26820 promoter, an Os09g11220 promoter, an Os04g21800         promoter, an Os10g23840 promoter, an Os08g13850 promoter, an         Os12g42980 promoter, an Os03g29280 promoter, an Os03g20650         promoter, or an Os06g43920 promoter (SEQ ID NO: 862-888,         respectively) or a Cauliflower Mosaic 35S promoter, or a         functional variant thereof, or a functional fragment thereof, or         a promoter sequence that is at least 80% identical to SEQ ID NO:         862-888; and/or         31. The method of embodiment 28, wherein the clade polypeptide         comprises any of SEQ ID NO: 2, 42, 86, 108, 126, 156, 192, 246,         278, 318, 356, 388, 410, or 444. † In the above embodiments 1,         9, 19, 24, and 26, greater photosynthetic resource use         efficiency may be characterized by or measured as, but is not         limited to, any one or more of following measurements or         characteristics relative to a control plant. The measured or         altered trait may be selected from the group consisting of:     -   (a) increased photosynthetic capacity, measured as an increase         in the rate of light-saturated photosynthesis of at least 5%,         10%, 15%, 20%, 25%, 30%, 35%, or 40% when compared to the rate         of light-saturated photosynthesis of a control leaf at the same         leaf-internal CO₂ concentration. Optionally, measurements are         made after 40 minutes of acclimation to a light intensity that         is saturating for photosynthesis; and/or     -   (b) increased photosynthetic rate, measured as an increase in         the rate of light-saturated photosynthesis of at least 5%, 10%,         15%, 19%, 20%, 22%, 23%, 25%, 30%, 32%, 35%, or 40%. Optionally,         measurements are made after 40 minutes of acclimation to a light         intensity known to be saturating for photosynthesis; and/or     -   (c) a decrease in the chlorophyll content of the leaf of at         least 5%, 10%, 15%, 20%, 25%, 30%, 35%, or 40%, observed in the         absence of a decrease in photosynthetic capacity; and/or     -   (d) a decrease in the percentage of the leaf dry weight that is         nitrogen of at least 0.5%, 1.0%, 1.5%, 2.0%, 2.5%, 3.0%, 3.5%,         or 4.0% observed in the absence of a decrease in photosynthetic         capacity or increase in dry weight; and/or     -   (e) increased transpiration efficiency, measured as an increase         in the rate of light-saturated photosynthesis relative to water         loss via transpiration from the leaf, of at least 5%, 10%, 15%,         20%, 25%, 30%, 35%, or 40%; optionally, measurements are made         after 40 minutes of acclimation to a light intensity of 700 μmol         PAR m⁻² s⁻¹; and/or     -   (f) an increase in the resistance to water vapor diffusion out         of the leaf that is exerted by the stomata, measured as a         decrease in stomatal conductance to H₂O loss from the leaf of at         least 5%, 10%, 15%, 20%, 25%, 30%, 35%, or 40%; optionally,         measurements were are after 40 minutes of acclimation to a light         intensity of 700 μmol PAR m−2 s−1; and/or     -   (g) a decrease in the resistance to carbon dioxide diffusion         into the leaf that is exerted by the stomata, measured as an         increase in stomatal conductance of at least 5%, 10%, 13%, 15%,         20%, 25%, 27%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, or 68%;         optionally, measurements were are after 40 minutes of         acclimation to a light intensity of 700 μmol PAR m−2 s−1; and/or     -   (h) a decrease in non-photochemical quenching of at least 2%, at         least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at         least 8%, at least 9%, or at least 10%, for leaf measurements         made after 40 minutes of acclimation to a light intensity of 700         μmol PAR m⁻² s⁻¹; and/or     -   (i) a decrease in the ratio of the carbon isotope ¹²C to ¹³C         found in either all the dried above-ground biomass, or specific         components of the above-ground biomass, e.g., leaves or         reproductive structures, of at least 0.5‰ (0.5 per mille), or at         least 1.0‰, 1.5‰, 2.0 ‰, 2.5‰, 3.0‰, 3.5‰, or 4.0‰ measured as a         decrease in the ratio of ¹²C to ¹³C relative to the controls         with both ratio being expressed relative to the same standard;         and/or     -   (j) an increase in the total dry weight of above-ground plant         material of at least 5%, 10%, 15%, 20%, 23%, 25%, 30%, 32%, 35%,         40%, 45%, 50%, 55%, 60%, 65%, 70%, or 75%.

All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

The present invention is not limited by the specific embodiments described herein. The invention now being fully described, it will be apparent to one of ordinary skill in the art that many changes and modifications can be made thereto without departing from the spirit or scope of the appended claims. Modifications that become apparent from the foregoing description and accompanying figures fall within the scope of the claims. 

What is claimed is:
 1. A transgenic plant having greater photosynthetic resource use efficiency than a control plant; wherein the transgenic plant comprises an exogenous recombinant polynucleotide comprising a photosynthetic tissue-enhanced promoter RBCS4 which is operably linked to a nucleic acid sequence that encodes a polypeptide comprising the amino acid sequence of SEQ ID NOs: 278; wherein the photosynthetic tissue-enhanced promoter RBCS4 regulates expression of the polypeptide in a photosynthetic tissue to a level that is effective in conferring greater photosynthetic resource use efficiency in the transgenic plant relative to the control plant; wherein the control plant does not comprise the recombinant polynucleotide; wherein the photosynthetic tissue-enhanced promoter RBCS4 does not regulate protein expression in a constitutive manner; and wherein expression of the polypeptide under the regulatory control of the photosynthetic tissue-enhanced promoter RBCS4 confers greater photosynthetic resource use efficiency in the transgenic plant relative to the control plant.
 2. The transgenic plant of claim 1, wherein the photosynthetic tissue-enhanced promoter RBCS4 is set forth in SEQ ID NO:
 863. 3. The transgenic plant of claim 1, wherein the transgenic plant has an altered trait, relative to the control plant, that confers the greater photosynthetic resource use efficiency, wherein the altered trait is selected from the group consisting of: (a) increased photosynthetic capacity, measured as an increase in the rate of light-saturated photosynthesis of at least 10% when compared to the rate of light-saturated photosynthesis of a control leaf at the same leaf-internal CO₂ concentration, with measurements made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; (b) increased photosynthetic rate, measured as an increase in the rate of light-saturated photosynthesis of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; (c) a decrease in the chlorophyll content of the leaf of at least 10%, observed in the absence of a decrease in photosynthetic capacity; (d) a decrease in the percentage of the leaf dry weight that is nitrogen of at least 0.5%, observed in the absence of a decrease in photosynthetic capacity or increase in dry weight; (e) increased transpiration efficiency, measured as an increase in the rate of light-saturated photosynthesis relative to water loss via transpiration from the leaf, of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (f) an increase in the resistance to water vapor diffusion out of the leaf that is exerted by the stomata, measured as a decrease in stomatal conductance to H₂O loss from the leaf of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (g) a decrease in the resistance to carbon dioxide diffusion into the leaf that is exerted by the stomata, measured as an increase in stomatal conductance of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (h) a decrease in the relative limitation that non-photochemical quenching exerts on the operation of PSII measured as a decrease in leaf non-photochemical quenching of at least 2% after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (i) a decrease in the ratio of the carbon isotope ¹²C to ¹³C found in either all the dried above-ground biomass, or specific components of the above-ground biomass, leaves, or reproductive structures, of at least 0.5‰ (0.5 per mille), measured as a decrease in the ratio of ¹²C to ¹³C relative to the controls with both ratio being expressed relative to the same standard; and (j) an increase in the total dry weight of above-ground plant material of at least 5%.
 4. The transgenic plant of claim 1, wherein a plurality of the transgenic plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density.
 5. The transgenic plant of claim 1, wherein the transgenic plant produces a greater yield than the control plant.
 6. The transgenic plant of claim 1, wherein the transgenic plant is selected from the group consisting of a dicot plant, monocot plant, corn, wheat, rice, Setaria, Miscanthus, switchgrass, ryegrass, sugarcane, miscane, barley, sorghum, turfgrass, soybean, cotton, canola, rapeseed, Crambe, Camelina, sugar beet, alfalfa, tomato, Eucalyptus, poplar, willow, pine, birch, and a woody plant.
 7. A method for increasing photosynthetic resource use efficiency in a plant, the method comprising: (a) providing one or more transgenic plants that comprise an exogenous recombinant polynucleotide comprising a photosynthetic tissue-enhanced promoter RBCS4 which is operably linked to a nucleic acid sequence that encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 278; wherein the photosynthetic tissue-enhanced promoter regulates expression of the polypeptide in a non-constitutive manner; and (b) growing the one or more transgenic plants; wherein expression of the polypeptide in the one or more transgenic plants confers increased photosynthetic resource use efficiency relative to a control plant that does not comprise the recombinant polynucleotide.
 8. The method of claim 7, wherein the photosynthetic tissue-enhanced promoter RBCS4 is set forth in SEQ ID NO:
 863. 9. The method of claim 7, wherein an expression cassette comprising the recombinant polynucleotide is introduced into a target plant to produce the transgenic plant.
 10. The method of claim 7, wherein the transgenic plant has an altered trait, relative to the control plant, that confers the greater photosynthetic resource use efficiency, wherein the altered trait is selected from the group consisting of: (a) increased photosynthetic capacity, measured as an increase in the rate of light-saturated photosynthesis of at least 10% when compared to the rate of light-saturated photosynthesis of a control leaf at the same leaf-internal CO₂ concentration, with measurements made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; (b) increased photosynthetic rate, measured as an increase in the rate of light-saturated photosynthesis of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; (c) a decrease in the chlorophyll content of the leaf of at least 10%, observed in the absence of a decrease in photosynthetic capacity; (d) a decrease in the percentage of the leaf dry weight that is nitrogen of at least 0.5%, observed in the absence of a decrease in photosynthetic capacity or increase in dry weight; (e) increased transpiration efficiency, measured as an increase in the rate of light-saturated photosynthesis relative to water loss via transpiration from the leaf, of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (f) an increase in the resistance to water vapor diffusion out of the leaf that is exerted by the stomata, measured as a decrease in stomatal conductance of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (g) a decrease in the resistance to carbon dioxide diffusion into the leaf that is exerted by the stomata, measured as an increase in stomatal conductance of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (h) a decrease in the relative limitation that non-photochemical quenching exerts on the operation of PSII measured as a decrease in leaf non-photochemical quenching of at least 2% after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (i) a decrease in the ratio of the carbon isotope ¹²C to ¹³C found in either all the dried above-ground biomass, or specific components of the above-ground biomass, leaves, or reproductive structures, of at least 0.5‰ (0.5 per mille), measured as a decrease in the ratio of ¹²C to ¹³C relative to the controls with both ratio being expressed relative to the same standard; (j) an increase in the total dry weight of above-ground plant material of at least 5%; and (k) increased yield.
 11. The method of claim 7, wherein the transgenic plant is selected for having the increased photosynthetic resource use efficiency relative to the control plant.
 12. The method of claim 7, wherein a plurality of the transgenic plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density.
 13. The method of claim 7, wherein the transgenic plant is selected from the group consisting of a dicot plant, monocot plant, corn, wheat, rice, Setaria, Miscanthus, switchgrass, ryegrass, sugarcane, miscane, barley, sorghum, turfgrass, soybean, cotton, canola, rapeseed, Crambe, Camelina, sugar beet, alfalfa, tomato, Eucalyptus, poplar, willow, pine, birch, and a woody plant.
 14. The method of claim 7, the method steps further including: crossing the target plant with itself, a second plant from the same line as the target plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed, wherein said transgenic seed comprises said exogenous recombinant polynucleotide.
 15. A method for producing and selecting a crop plant with greater yield or photosynthetic resource use efficiency than a control plant, the method comprising: (a) providing one or more transgenic plants that comprise an exogenous recombinant polynucleotide that comprises a photosynthetic tissue-enhanced promoter RBCS4 which is operably linked to a nucleic acid sequence that encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 278, and wherein the photosynthetic tissue-enhanced promoter does not regulate protein expression in a constitutive manner; (b) growing a plurality of the transgenic plants; and (c) selecting a transgenic plant from the step (b) that has greater photosynthetic resource use efficiency than the control plant, wherein the control plant does not comprise the recombinant polynucleotide and wherein expression of the polypeptide in the selected transgenic plant confers the greater yield of the selected transgenic plant relative to the control plant.
 16. The method of claim 15, the method steps further including: (d) crossing the selected transgenic plant with itself, a second plant from the same line as the selected transgenic plant, a non-transgenic plant, a wild-type plant, or a transgenic plant from a different line of plants, to produce a transgenic seed, wherein the transgenic seed comprises said exogenous recombinant polynucleotide.
 17. The method of claim 15, wherein a plurality of the selected transgenic plants have greater cumulative canopy photosynthesis than the canopy photosynthesis of the same number of the control plants grown under the same conditions and at the same density.
 18. The method of claim 15, wherein the selected transgenic plant has an altered trait, relative to the control plant, that confers the greater photosynthetic resource use efficiency, wherein the altered trait is selected from the group consisting of: (a) increased photosynthetic capacity, measured as an increase in the rate of light-saturated photosynthesis of at least 10% when compared to the rate of light-saturated photosynthesis of a control leaf at the same leaf-internal CO₂ concentration, with measurements made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; (b) increased photosynthetic rate, measured as an increase in the rate of light-saturated photosynthesis of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity that is saturating for photosynthesis; (c) a decrease in the chlorophyll content of the leaf of at least 10%, observed in the absence of a decrease in photosynthetic capacity; (d) a decrease in the percentage of the leaf dry weight that is nitrogen of at least 0.5%, observed in the absence of a decrease in photosynthetic capacity or increase in dry weight; (e) increased transpiration efficiency, measured as an increase in the rate of light-saturated photosynthesis relative to water loss via transpiration from the leaf, of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (f) an increase in the resistance to water vapor diffusion out of the leaf that is exerted by the stomata, measured as a decrease in stomatal conductance of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (g) a decrease in the resistance to carbon dioxide diffusion into the leaf that is exerted by the stomata, measured as an increase in stomatal conductance of at least 10%, with measurements made after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (h) a decrease in the relative limitation that non-photochemical quenching exerts on the operation of PSII measured as a decrease in leaf non-photochemical quenching of at least 2% after 40 minutes of acclimation to a light intensity of 700 μmol PAR m⁻² s⁻¹; (i) a decrease in the ratio of the carbon isotope ¹²C to ¹³C found in either all the dried above-ground biomass, or specific components of the above-ground biomass, leaves, or reproductive structures, of at least 0.5‰ (0.5 per mille), measured as a decrease in the ratio of ¹²C to ¹³C relative to the controls with both ratio being expressed relative to the same standard; and (j) an increase in the total dry weight of above-ground plant material of at least 5%. 